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seqret |
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Function
Read and write (return) sequencesDescription
seqret reads in one or more sequences and writes them out again. The sequence input may be a literal sequence or read from a database, file, file of sequence names, or even the command-line or the output of another programs. The sequence output can be written to screen, to file, or passed to another program. A wide range of standard sequence formats may be specified for input and output. If you don't specify the input format, seqret will try a set of possible formats until it reads it in successfully. The sequence input and output, as for all EMBOSS programs, is described by a Uniform Sequence Address. This is is a very flexible way of specifying one or more sequences from a variety of sources and includes sequence files, database queries and external applications.
There are many options built-in into EMBOSS for detailed specification of the input and output sequences, for example the sequence type, file format. specification of sequence regions by begin and end positions, or generation of the reverse complement of a nucleic acid sequence. On output seqret can change the case of the sequence to upper or to lower case.
seqret is useful for a variety of tasks, including extracting sequences from databases, displaying sequences, reformatting sequences, producing the reverse complement of a sequence, extracting fragments of a sequence, sequence case conversion or any combination of the above functions.
Usage
Here is a sample session with seqretExtract an entry from a database and write it to a file:
% seqret Read and write (return) sequences Input (gapped) sequence(s): tembl:x65923 output sequence(s) [x65923.fasta]: |
Go to the input files for this example
Go to the output files for this example
Example 2
Read all entries in the database 'tembl' that start with 'ab' and write them to a file. In this example the specification is all done in the command line and to stop Unix getting confused by the '*' character, it has to have a backslash ('\') before it:
% seqret "tembl:ab*" aball.seq Read and write (return) sequences |
Go to the output files for this example
Example 3
seqret does not read in features by default because this results in slightly faster performance. If however you wish to read in features with your sequence and write them out on output, using '-feature' will change the default behaviour to use any features present in the sequence. N.B. use embl format for the output file as the default format 'fasta' reports the features in gff (file "<seqname>.gff")
% seqret -feature Read and write (return) sequences Input (gapped) sequence(s): tembl:x65923 output sequence(s) [x65923.fasta]: embl::x65923.embl |
Go to the output files for this example
Example 4
Display the contents of the sequence on the screen:
% seqret Read and write (return) sequences Input (gapped) sequence(s): tembl:x65923 output sequence(s) [x65923.fasta]: stdout >X65923 X65923.1 H.sapiens fau mRNA ttcctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgc agctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcg cccagatcaaggctcatgtagcctcactggagggcattgccccggaagatcaagtcgtgc tcctggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggccc tgactaccctggaagtagcaggccgcatgcttggaggtaaagttcatggttccctggccc gtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaagaaga agacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtgccca cctttggcaagaagaagggccccaatgccaactcttaagtcttttgtaattctggctttc tctaataaaaaagccacttagttcagtcaaaaaaaaaa |
Example 5
Write the result in GCG format by using the qualifier '-osformat'.
% seqret -osf gcg Read and write (return) sequences Input (gapped) sequence(s): tembl:x65923 output sequence(s) [x65923.gcg]: |
Go to the output files for this example
Example 6
Write the result in GCG format by specifying the format in the output USA on the command line.
% seqret -outseq gcg::x65923.gcg Read and write (return) sequences Input (gapped) sequence(s): tembl:x65923 |
Example 7
Write the result in GCG format by specifying the format in the output USA at the prompt.
% seqret Read and write (return) sequences Input (gapped) sequence(s): tembl:x65923 output sequence(s) [x65923.fasta]: gcg::x65923.gcg |
Example 8
Write the reverse-complement of a sequence:
% seqret -srev Read and write (return) sequences Input (gapped) sequence(s): tembl:x65923 output sequence(s) [x65923.fasta]: |
Go to the output files for this example
Example 9
Extract the bases between the positions starting at 5 and ending at 25:
% seqret -sbegin 5 -send 25 Read and write (return) sequences Input (gapped) sequence(s): tembl:x65923 output sequence(s) [x65923.fasta]: |
Go to the output files for this example
Example 10
Extract the bases between the positions starting at 5 and ending at 5 bases before the end of the sequence:
% seqret -sbegin 5 -send -5 Read and write (return) sequences Input (gapped) sequence(s): tembl:x65923 output sequence(s) [x65923.fasta]: |
Go to the output files for this example
Example 11
Read all entries in the database 'tembl' that start with 'h' and write them to a file:
% seqret Read and write (return) sequences Input (gapped) sequence(s): tembl:h* output sequence(s) [h45989.fasta]: hall.seq |
Go to the output files for this example
Command line arguments
Read and write (return) sequences
Version: EMBOSS:6.6.0.0
Standard (Mandatory) qualifiers:
[-sequence] seqall (Gapped) sequence(s) filename and optional
format, or reference (input USA)
[-outseq] seqoutall [
|
| Qualifier | Type | Description | Allowed values | Default |
|---|---|---|---|---|
| Standard (Mandatory) qualifiers | ||||
| [-sequence] (Parameter 1) |
seqall | (Gapped) sequence(s) filename and optional format, or reference (input USA) | Readable sequence(s) | Required |
| [-outseq] (Parameter 2) |
seqoutall | Sequence set(s) filename and optional format (output USA) | Writeable sequence(s) | <*>.format |
| Additional (Optional) qualifiers | ||||
| (none) | ||||
| Advanced (Unprompted) qualifiers | ||||
| -feature | boolean | Use feature information | Boolean value Yes/No | No |
| -firstonly | boolean | Read one sequence and stop | Boolean value Yes/No | No |
| Associated qualifiers | ||||
| "-sequence" associated seqall qualifiers | ||||
| -sbegin1 -sbegin_sequence |
integer | Start of each sequence to be used | Any integer value | 0 |
| -send1 -send_sequence |
integer | End of each sequence to be used | Any integer value | 0 |
| -sreverse1 -sreverse_sequence |
boolean | Reverse (if DNA) | Boolean value Yes/No | N |
| -sask1 -sask_sequence |
boolean | Ask for begin/end/reverse | Boolean value Yes/No | N |
| -snucleotide1 -snucleotide_sequence |
boolean | Sequence is nucleotide | Boolean value Yes/No | N |
| -sprotein1 -sprotein_sequence |
boolean | Sequence is protein | Boolean value Yes/No | N |
| -slower1 -slower_sequence |
boolean | Make lower case | Boolean value Yes/No | N |
| -supper1 -supper_sequence |
boolean | Make upper case | Boolean value Yes/No | N |
| -scircular1 -scircular_sequence |
boolean | Sequence is circular | Boolean value Yes/No | N |
| -squick1 -squick_sequence |
boolean | Read id and sequence only | Boolean value Yes/No | N |
| -sformat1 -sformat_sequence |
string | Input sequence format | Any string | |
| -iquery1 -iquery_sequence |
string | Input query fields or ID list | Any string | |
| -ioffset1 -ioffset_sequence |
integer | Input start position offset | Any integer value | 0 |
| -sdbname1 -sdbname_sequence |
string | Database name | Any string | |
| -sid1 -sid_sequence |
string | Entryname | Any string | |
| -ufo1 -ufo_sequence |
string | UFO features | Any string | |
| -fformat1 -fformat_sequence |
string | Features format | Any string | |
| -fopenfile1 -fopenfile_sequence |
string | Features file name | Any string | |
| "-outseq" associated seqoutall qualifiers | ||||
| -osformat2 -osformat_outseq |
string | Output seq format | Any string | |
| -osextension2 -osextension_outseq |
string | File name extension | Any string | |
| -osname2 -osname_outseq |
string | Base file name | Any string | |
| -osdirectory2 -osdirectory_outseq |
string | Output directory | Any string | |
| -osdbname2 -osdbname_outseq |
string | Database name to add | Any string | |
| -ossingle2 -ossingle_outseq |
boolean | Separate file for each entry | Boolean value Yes/No | N |
| -oufo2 -oufo_outseq |
string | UFO features | Any string | |
| -offormat2 -offormat_outseq |
string | Features format | Any string | |
| -ofname2 -ofname_outseq |
string | Features file name | Any string | |
| -ofdirectory2 -ofdirectory_outseq |
string | Output directory | Any string | |
| General qualifiers | ||||
| -auto | boolean | Turn off prompts | Boolean value Yes/No | N |
| -stdout | boolean | Write first file to standard output | Boolean value Yes/No | N |
| -filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N |
| -options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N |
| -debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N |
| -verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y |
| -help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N |
| -warning | boolean | Report warnings | Boolean value Yes/No | Y |
| -error | boolean | Report errors | Boolean value Yes/No | Y |
| -fatal | boolean | Report fatal errors | Boolean value Yes/No | Y |
| -die | boolean | Report dying program messages | Boolean value Yes/No | Y |
| -version | boolean | Report version number and exit | Boolean value Yes/No | N |
Input file format
seqret reads one or more nucleotide or protein sequences.
The input is a standard EMBOSS sequence query (also known as a 'USA').
Major sequence database sources defined as standard in EMBOSS installations include srs:embl, srs:uniprot and ensembl
Data can also be read from sequence output in any supported format written by an EMBOSS or third-party application.
The input format can be specified by using the command-line qualifier -sformat xxx, where 'xxx' is replaced by the name of the required format. The available format names are: gff (gff3), gff2, embl (em), genbank (gb, refseq), ddbj, refseqp, pir (nbrf), swissprot (swiss, sw), dasgff and debug.
See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further information on sequence formats.
Input files for usage example
'tembl:x65923' is a sequence entry in the example nucleic acid database 'tembl'
Database entry: tembl:x65923
ID X65923; SV 1; linear; mRNA; STD; HUM; 518 BP.
XX
AC X65923;
XX
DT 13-MAY-1992 (Rel. 31, Created)
DT 18-APR-2005 (Rel. 83, Last updated, Version 11)
XX
DE H.sapiens fau mRNA
XX
KW fau gene.
XX
OS Homo sapiens (human)
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC Homo.
XX
RN [1]
RP 1-518
RA Michiels L.M.R.;
RT ;
RL Submitted (29-APR-1992) to the INSDC.
RL L.M.R. Michiels, University of Antwerp, Dept of Biochemistry,
RL Universiteisplein 1, 2610 Wilrijk, BELGIUM
XX
RN [2]
RP 1-518
RX PUBMED; 8395683.
RA Michiels L., Van der Rauwelaert E., Van Hasselt F., Kas K., Merregaert J.;
RT "fau cDNA encodes a ubiquitin-like-S30 fusion protein and is expressed as
RT an antisense sequence in the Finkel-Biskis-Reilly murine sarcoma virus";
RL Oncogene 8(9):2537-2546(1993).
XX
DR Ensembl-Gn; ENSG00000149806; Homo_sapiens.
DR Ensembl-Tr; ENST00000279259; Homo_sapiens.
DR Ensembl-Tr; ENST00000434372; Homo_sapiens.
DR Ensembl-Tr; ENST00000525297; Homo_sapiens.
DR Ensembl-Tr; ENST00000526555; Homo_sapiens.
DR Ensembl-Tr; ENST00000527548; Homo_sapiens.
DR Ensembl-Tr; ENST00000529259; Homo_sapiens.
DR Ensembl-Tr; ENST00000529639; Homo_sapiens.
DR Ensembl-Tr; ENST00000531743; Homo_sapiens.
XX
FH Key Location/Qualifiers
FH
FT source 1..518
FT /organism="Homo sapiens"
FT /chromosome="11q"
FT /map="13"
FT /mol_type="mRNA"
FT /clone_lib="cDNA"
FT /clone="pUIA 631"
FT /tissue_type="placenta"
FT /db_xref="taxon:9606"
FT misc_feature 57..278
FT /note="ubiquitin like part"
FT CDS 57..458
FT /gene="fau"
FT /db_xref="GDB:135476"
FT /db_xref="GOA:P35544"
FT /db_xref="GOA:P62861"
FT /db_xref="H-InvDB:HIT000322806.14"
FT /db_xref="HGNC:3597"
FT /db_xref="InterPro:IPR000626"
FT /db_xref="InterPro:IPR006846"
FT /db_xref="InterPro:IPR019954"
FT /db_xref="InterPro:IPR019955"
FT /db_xref="InterPro:IPR019956"
FT /db_xref="PDB:2L7R"
FT /db_xref="UniProtKB/Swiss-Prot:P35544"
FT /db_xref="UniProtKB/Swiss-Prot:P62861"
FT /protein_id="CAA46716.1"
FT /translation="MQLFVRAQELHTFEVTGQETVAQIKAHVASLEGIAPEDQVVLLAG
FT APLEDEATLGQCGVEALTTLEVAGRMLGGKVHGSLARAGKVRGQTPKVAKQEKKKKKTG
FT RAKRRMQYNRRFVNVVPTFGKKKGPNANS"
FT misc_feature 98..102
FT /note="nucleolar localization signal"
FT misc_feature 279..458
FT /note="S30 part"
FT polyA_signal 484..489
FT polyA_site 509
XX
SQ Sequence 518 BP; 125 A; 139 C; 148 G; 106 T; 0 other;
ttcctctttc tcgactccat cttcgcggta gctgggaccg ccgttcagtc gccaatatgc 60
agctctttgt ccgcgcccag gagctacaca ccttcgaggt gaccggccag gaaacggtcg 120
cccagatcaa ggctcatgta gcctcactgg agggcattgc cccggaagat caagtcgtgc 180
tcctggcagg cgcgcccctg gaggatgagg ccactctggg ccagtgcggg gtggaggccc 240
tgactaccct ggaagtagca ggccgcatgc ttggaggtaa agttcatggt tccctggccc 300
gtgctggaaa agtgagaggt cagactccta aggtggccaa acaggagaag aagaagaaga 360
agacaggtcg ggctaagcgg cggatgcagt acaaccggcg ctttgtcaac gttgtgccca 420
cctttggcaa gaagaagggc cccaatgcca actcttaagt cttttgtaat tctggctttc 480
tctaataaaa aagccactta gttcagtcaa aaaaaaaa 518
//
|
Output file format
The output is a standard EMBOSS sequence file.
The results can be output in one of several styles by using the command-line qualifier -osformat xxx, where 'xxx' is replaced by the name of the required format. The available format names are: embl, genbank, gff, pir, swiss, dasgff, debug, listfile, dbmotif, diffseq, excel, feattable, motif, nametable, regions, seqtable, simple, srs, table, tagseq.
See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further information on sequence formats.
The output from seqret is one or more sequences, and by default will be written in FASTA format.
If the '-firstonly' qualifier is used then only the first sequence of the input USA specification will be written out.
In some cases the output filename will be the same as the input filename, but as seqret reads only the first sequence before opening the output file it may try to overwrite the input. Note that this is not true of seqretset which reads all sequences into memory at startup, but which can need a large amount of memory for many sequences.
Output files for usage example
File: x65923.fasta
>X65923 X65923.1 H.sapiens fau mRNA ttcctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgc agctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcg cccagatcaaggctcatgtagcctcactggagggcattgccccggaagatcaagtcgtgc tcctggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggccc tgactaccctggaagtagcaggccgcatgcttggaggtaaagttcatggttccctggccc gtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaagaaga agacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtgccca cctttggcaagaagaagggccccaatgccaactcttaagtcttttgtaattctggctttc tctaataaaaaagccacttagttcagtcaaaaaaaaaa |
Output files for usage example 2
File: aball.seq
>AB009602 AB009602.1 Schizosaccharomyces pombe mRNA for MET1 homolog, partial cds. gttcgatgcctaaaataccttcttttgtccctacacagaccacagttttcctaatggctt tacaccgactagaaattcttgtgcaagcactaattgaaagcggttggcctagagtgttac cggtttgtatagctgagcgcgtctcttgccctgatcaaaggttcattttctctactttgg aagacgttgtggaagaatacaacaagtacgagtctctcccccctggtttgctgattactg gatacagttgtaatacccttcgcaacaccgcgtaactatctatatgaattattttccctt tattatatgtagtaggttcgtctttaatcttcctttagcaagtcttttactgttttcgac ctcaatgttcatgttcttaggttgttttggataatatgcggtcagtttaatcttcgttgt ttcttcttaaaatatttattcatggtttaatttttggtttgtacttgttcaggggccagt tcattatttactctgtttgtatacagcagttcttttatttttagtatgattttaatttaa aacaattctaatggtcaaaaa >AB000095 AB000095.1 Homo sapiens mRNA for hepatocyte growth factor activator inhibitor, complete cds. cggccgagcccagctctccgagcaccgggtcggaagccgcgacccgagccgcgcaggaag ctgggaccggaacctcggcggacccggccccacccaactcacctgcgcaggtcaccagca ccctcggaacccagaggcccgcgctctgaaggtgacccccctggggaggaaggcgatggc ccctgcgaggacgatggcccgcgcccgcctcgccccggccggcatccctgccgtcgcctt gtggcttctgtgcacgctcggcctccagggcacccaggccgggccaccgcccgcgccccc tgggctgcccgcgggagccgactgcctgaacagctttaccgccggggtgcctggcttcgt gctggacaccaacgcctcggtcagcaacggagctaccttcctggagtcccccaccgtgcg ccggggctgggactgcgtgcgcgcctgctgcaccacccagaactgcaacttggcgctagt ggagctgcagcccgaccgcggggaggacgccatcgccgcctgcttcctcatcaactgcct ctacgagcagaacttcgtgtgcaagttcgcgcccagggagggcttcatcaactacctcac gagggaagtgtaccgctcctaccgccagctgcggacccagggctttggagggtctgggat ccccaaggcctgggcaggcatagacttgaaggtacaaccccaggaacccctggtgctgaa ggatgtggaaaacacagattggcgcctactgcggggtgacacggatgtcagggtagagag gaaagacccaaaccaggtggaactgtggggactcaaggaaggcacctacctgttccagct gacagtgactagctcagaccacccagaggacacggccaacgtcacagtcactgtgctgtc caccaagcagacagaagactactgcctcgcatccaacaaggtgggtcgctgccggggctc tttcccacgctggtactatgaccccacggagcagatctgcaagagtttcgtttatggagg ctgcttgggcaacaagaacaactaccttcgggaagaagagtgcattctagcctgtcgggg tgtgcaaggcccctccatggaaaggcgccatccagtgtgctctggcacctgtcagcccac ccagttccgctgcagcaatggctgctgcatcgacagtttcctggagtgtgacgacacccc caactgccccgacgcctccgacgaggctgcctgtgaaaaatacacgagtggctttgacga gctccagcgcatccatttccccagtgacaaagggcactgcgtggacctgccagacacagg actctgcaaggagagcatcccgcgctggtactacaaccccttcagcgaacactgcgcccg ctttacctatggtggttgttatggcaacaagaacaactttgaggaagagcagcagtgcct cgagtcttgtcgcggcatctccaagaaggatgtgtttggcctgaggcgggaaatccccat tcccagcacaggctctgtggagatggctgtcgcagtgttcctggtcatctgcattgtggt ggtggtagccatcttgggttactgcttcttcaagaaccagagaaaggacttccacggaca ccaccaccacccaccacccacccctgccagctccactgtctccactaccgaggacacgga gcacctggtctataaccacaccacccggcccctctgagcctgggtctcaccggctctcac ctggccctgcttcctgcttgccaaggcagaggcctgggctgggaaaaactttggaaccag actcttgcctgtttcccaggcccactgtgcctcagagaccagggctccagcccctcttgg agaagtctcagctaagctcacgtcctgagaaagctcaaaggtttggaaggagcagaaaac ccttgggccagaagtaccagactagatggacctgcctgcataggagtttggaggaagttg gagttttgtttcctctgttcaaagctgcctgtccctaccccatggtgctaggaagaggag tggggtggtgtcagaccctggaggccccaaccctgtcctcccgagctcctcttccatgct gtgcgcccagggctgggaggaaggacttccctgtgtagtttgtgctgtaaagagttgctt tttgtttatttaatgctgtggcatgggtgaagaggaggggaagaggcctgtttggcctct ctgtcctctcttcctcttcccccaagattgagctctctgcccttgatcagccccaccctg [Part of this file has been deleted for brevity] ccttgtcaggcggaagggcatcaacggcgggcttctcccgctgggcctgagcccgttgat ctccccaagctgcaagcgaaccttgcgggtcaaggtcgagggcaatcacggattcccctg cctctgtggccgcgacggcaatggcagcagcgagggtagtttttcccgcgccgcccttct gcgtgaccagagcaattgtcttcatgcctgcactatagcattaaggcactaaagcgtcaa agcgccatagcggcatagcggcatagcggcatagcgctaaaatgctatagcattattaaa tacagcgctacagcgctataatgctgcaacggttaggaccgcaatttgcgccccgggccg gttgcgctatcgaccagctcaattaactgctcgggctcggacgcgaaccacgcgaagctg ccccaagccaaggagtcgagggagccacggttgatgagagctttgttgtaggtggaccag ttggtgattttgaacttttgctttgccacggaacggtctgcgttgtcgggaagatgcgtg atctgatccttcaactcagcaaaagttcgatttattcaacaaagccacgttgtgtctcaa aatctctgatgttacattgcacaagataaaaatatatcatcatgaacaataaaactgtct gcttacataaacagtaatacaaggggtgttatgagccatattcaacgggaaacgtcttgc tcgaagccgcgattaaattccaacatggatgctgatttatatgggtataaatgggctcgc gataatgtcgggcaatcaggtgcgacaatctatcgattgtatgggaagcccgatgcgcca gagttgtttctgaaacatggcaaaggtagcgttgccaatgatgttacagatgagatggtc agactaaactggctgacggaatttatgcctcttccgaccatcaagcattttatccgtact cctgatgatgcatggttactcaccactgcgatccccgggaaaacagcattccaggtatta gaagaatatcctgattcaggtgaaaatattgttgatgcgctggcagtgttcctgcgccgg ttgcattcgattcctgtttgtaattgtccttttaacagcgatcgcgtatttcgtctcgct caggcgcaatcacgaatgaataacggtttggttgatgcgagtgattttgatgacgagcgt aatggctggcctgttgaacaagtctggaaagaaatgcataagcttttgccattctcaccg gattcagtcgtcactcatggtgatttctcacttgataaccttatttttgacgaggggaaa ttaataggttgtattgatgttggacgagtcggaatcgcagaccgataccaggatcttgcc atcctatggaactgcctcggtgagttttctccttcattacagaaacggctttttcaaaaa tatggtattgataatcctgatatgaataaattgcagtttcatttgatgctcgatgagttt ttctaatcagaattggttaattggttgtaacactggcagagcattacgctgacttgacgg gacggcggctttgttgaataaatcgcattcgccattcaggctgcgcaactgttgggaagg gcgatcggtgcgggcctcttcgctattacgccagctggcgaaagggggatgtgctgcaag gcgattaagttgggtaacgccagggttttcccagtcacgacgttgtaaaacgacggccag tgccaagcttgcatgcctgcaggtcgactctagaggatccccgggtaccgagctcgaatt cgtaatcatggtcatagctgtttcctgtgtgaaattgttatccgctcacaattccacaca acatacgagccggaagcataaagtgtaaagcctggggtgcctaatgagtgagctaactca cattaattgcgttgcgctcactgcccgctttccagtcgggaaacctgtcgtgccagctgc attaatgaatcggccaacgcgcggggagaggcggtttgcgtattggcgaacttttgctga gttgaaggatcagatcacgcatcttcccgacaacgcagaccgttccgtggcaaagcaaaa gttcaaaatcagtaaccgtcagtgccgataagttcaaagttaaacctggtgttgatacca acattgaaacgctgatcgaaaacgcgctgaaaaacgctgctgaatgtgcgagcttcttcc gcttcctcgctcactgactcgctgcgctcggtcgttcggctgcggcgagcggtatcagct cactcaaaggcggtaatacggttatccacagaatcaggggataacgcaggaaagaacatg tgagcaaaaggccagcaaaaggccaggaaccgtaaaaaggccgcgttgctggcgtttttc cataggctccgcccccctgacgagcatcacaaaaatcgacgctcaagtcagaggtggcga aacccgacaggactataaagataccaggcgtttccccctggaagctccctcgtgcgctct cctgttccgaccctgccgcttaccggatacctgtccgcctttctcccttcgggaagcgtg gcgctttctcaatgctcacgctgtaggtatctcagttcggtgtaggtcgttcgctccaag ctgggctgtgtgcacgaaccccccgttcagcccgaccgctgcgccttatccggtaactat cgtcttgagtccaacccggtaagacacgacttatcgccactggcagcagccactggtaac aggattagcagagcgaggtatgtaggcggtgctacagagttcttgaagtggtggcctaac tacggctacactagaaggacagtatttggtatctgcgctctgctgaagccagttaccttc ggaaaaagagttggtagctcttgatccggcaaacaaaccaccgctggtagcggtggtttt tttgtttgcaagcagcagattacgcgcagaaaaaaaggatctcaagaagatcctttgatc ttttctacggggtctgacgctcagtggaacgatccgtcga |
Output files for usage example 3
File: x65923.embl
ID X65923; SV 1; linear; mRNA; STD; HUM; 518 BP.
XX
AC X65923;
XX
DT 13-MAY-1992 (Rel. 31, Created)
DT 18-APR-2005 (Rel. 83, Last updated, Version 11)
XX
DE H.sapiens fau mRNA
XX
KW fau gene.
XX
OS Homo sapiens (human)
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC Homo.
XX
RN [1]
RP 1-518
RA Michiels L.M.R.;
RT ;
RL Submitted (29-APR-1992) to the INSDC.
RL L.M.R. Michiels, University of Antwerp, Dept of Biochemistry,
RL Universiteisplein 1, 2610 Wilrijk, BELGIUM.
XX
RN [2]
RP 1-518
RX PUBMED; 8395683.
RA Michiels L., Van der Rauwelaert E., Van Hasselt F., Kas K., Merregaert J.;
RT "fau cDNA encodes a ubiquitin-like-S30 fusion protein and is expressed as
RT an antisense sequence in the Finkel-Biskis-Reilly murine sarcoma virus";
RL Oncogene 8(9):2537-2546(1993).
XX
DR Ensembl-Gn; ENSG00000149806; Homo_sapiens.
DR Ensembl-Tr; ENST00000279259; Homo_sapiens.
DR Ensembl-Tr; ENST00000434372; Homo_sapiens.
DR Ensembl-Tr; ENST00000525297; Homo_sapiens.
DR Ensembl-Tr; ENST00000526555; Homo_sapiens.
DR Ensembl-Tr; ENST00000527548; Homo_sapiens.
DR Ensembl-Tr; ENST00000529259; Homo_sapiens.
DR Ensembl-Tr; ENST00000529639; Homo_sapiens.
DR Ensembl-Tr; ENST00000531743; Homo_sapiens.
XX
FH Key Location/Qualifiers
FH
FT source 1..518
FT /organism="Homo sapiens"
FT /chromosome="11q"
FT /map="13"
FT /mol_type="mRNA"
FT /clone_lib="cDNA"
FT /clone="pUIA 631"
FT /tissue_type="placenta"
FT /db_xref="taxon:9606"
FT misc_feature 57..278
FT /note="ubiquitin like part"
FT CDS 57..458
FT /gene="fau"
FT /db_xref="GDB:135476"
FT /db_xref="GOA:P35544"
FT /db_xref="GOA:P62861"
FT /db_xref="H-InvDB:HIT000322806.14"
FT /db_xref="HGNC:3597"
FT /db_xref="InterPro:IPR000626"
FT /db_xref="InterPro:IPR006846"
FT /db_xref="InterPro:IPR019954"
FT /db_xref="InterPro:IPR019955"
FT /db_xref="InterPro:IPR019956"
FT /db_xref="PDB:2L7R"
FT /db_xref="UniProtKB/Swiss-Prot:P35544"
FT /db_xref="UniProtKB/Swiss-Prot:P62861"
FT /protein_id="CAA46716.1"
FT /translation="MQLFVRAQELHTFEVTGQETVAQIKAHVASLEGIAPEDQVVLLAG
FT APLEDEATLGQCGVEALTTLEVAGRMLGGKVHGSLARAGKVRGQTPKVAKQEKKKKKTG
FT RAKRRMQYNRRFVNVVPTFGKKKGPNANS"
FT misc_feature 98..102
FT /note="nucleolar localization signal"
FT misc_feature 279..458
FT /note="S30 part"
FT polyA_signal 484..489
FT polyA_site 509
XX
SQ Sequence 518 BP; 125 A; 139 C; 148 G; 106 T; 0 other;
ttcctctttc tcgactccat cttcgcggta gctgggaccg ccgttcagtc gccaatatgc 60
agctctttgt ccgcgcccag gagctacaca ccttcgaggt gaccggccag gaaacggtcg 120
cccagatcaa ggctcatgta gcctcactgg agggcattgc cccggaagat caagtcgtgc 180
tcctggcagg cgcgcccctg gaggatgagg ccactctggg ccagtgcggg gtggaggccc 240
tgactaccct ggaagtagca ggccgcatgc ttggaggtaa agttcatggt tccctggccc 300
gtgctggaaa agtgagaggt cagactccta aggtggccaa acaggagaag aagaagaaga 360
agacaggtcg ggctaagcgg cggatgcagt acaaccggcg ctttgtcaac gttgtgccca 420
cctttggcaa gaagaagggc cccaatgcca actcttaagt cttttgtaat tctggctttc 480
tctaataaaa aagccactta gttcagtcaa aaaaaaaa 518
//
|
Output files for usage example 5
File: x65923.gcg
!!NA_SEQUENCE 1.0 H.sapiens fau mRNA X65923 Length: 518 Type: N Check: 2981 .. 1 ttcctctttc tcgactccat cttcgcggta gctgggaccg ccgttcagtc 51 gccaatatgc agctctttgt ccgcgcccag gagctacaca ccttcgaggt 101 gaccggccag gaaacggtcg cccagatcaa ggctcatgta gcctcactgg 151 agggcattgc cccggaagat caagtcgtgc tcctggcagg cgcgcccctg 201 gaggatgagg ccactctggg ccagtgcggg gtggaggccc tgactaccct 251 ggaagtagca ggccgcatgc ttggaggtaa agttcatggt tccctggccc 301 gtgctggaaa agtgagaggt cagactccta aggtggccaa acaggagaag 351 aagaagaaga agacaggtcg ggctaagcgg cggatgcagt acaaccggcg 401 ctttgtcaac gttgtgccca cctttggcaa gaagaagggc cccaatgcca 451 actcttaagt cttttgtaat tctggctttc tctaataaaa aagccactta 501 gttcagtcaa aaaaaaaa |
Output files for usage example 8
File: x65923.fasta
>X65923 X65923.1 H.sapiens fau mRNA ttttttttttgactgaactaagtggcttttttattagagaaagccagaattacaaaagac ttaagagttggcattggggcccttcttcttgccaaaggtgggcacaacgttgacaaagcg ccggttgtactgcatccgccgcttagcccgacctgtcttcttcttcttcttctcctgttt ggccaccttaggagtctgacctctcacttttccagcacgggccagggaaccatgaacttt acctccaagcatgcggcctgctacttccagggtagtcagggcctccaccccgcactggcc cagagtggcctcatcctccaggggcgcgcctgccaggagcacgacttgatcttccggggc aatgccctccagtgaggctacatgagccttgatctgggcgaccgtttcctggccggtcac ctcgaaggtgtgtagctcctgggcgcggacaaagagctgcatattggcgactgaacggcg gtcccagctaccgcgaagatggagtcgagaaagaggaa |
Output files for usage example 9
File: x65923.fasta
>X65923 X65923.1 H.sapiens fau mRNA tctttctcgactccatcttcg |
Output files for usage example 10
File: x65923.fasta
>X65923 X65923.1 H.sapiens fau mRNA tctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgcagct ctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcgccca gatcaaggctcatgtagcctcactggagggcattgccccggaagatcaagtcgtgctcct ggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggccctgac taccctggaagtagcaggccgcatgcttggaggtaaagttcatggttccctggcccgtgc tggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaagaagaagac aggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtgcccacctt tggcaagaagaagggccccaatgccaactcttaagtcttttgtaattctggctttctcta ataaaaaagccacttagttcagtcaaaaaa |
Output files for usage example 11
File: hall.seq
>H45989 H45989.1 yo13c02.s1 Soares adult brain N2b5HB55Y Homo sapiens cDNA clone IMAGE:177794 3', mRNA sequence. ccggnaagctcancttggaccaccgactctcgantgnntcgccgcgggagccggntggan aacctgagcgggactggnagaaggagcagagggaggcagcacccggcgtgacggnagtgt gtggggcactcaggccttccgcagtgtcatctgccacacggaaggcacggccacgggcag gggggtctatgatcttctgcatgcccagctggcatggccccacgtagagtggnntggcgt ctcggtgctggtcagcgacacgttgtcctggctgggcaggtccagctcccggaggacctg gggcttcagcttcccgtagcgctggctgcagtgacggatgctcttgcgctgccatttctg ggtgctgtcactgtccttgctcactccaaaccagttcggcggtccccctgcggatggtct gtgttgatggacgtttgggctttgcagcaccggccgccgagttcatggtngggtnaagag atttgggttttttcn |
Data files
None.Notes
This description of what you can do when reading or writing files is not specific to the program seqret. All EMBOSS programs that read or write sequences can do the same.seqret is often one of the first programs taught in EMBOSS training courses. This is because it is versatile, it is extremely powerful for its size (17 lines of code) it illustrates many aspects of EMBOSS programs and it was one of the first EMBOSS programs to be written, so it has a special place in the hearts of EMBOSS developers.
The name 'seqret' derives both from its function ("sequence return") and from the fact that immense amounts of functionality can come from so few lines of source code - most of the work is done by the EMBOSS libraries which the program calls and whose complexity is hidden, or "secret".
The simplicity of the above description of this program greatly understates the rich functionality of this program.
Because EMBOSS programs can take a wide range of qualifiers that slightly change the behaviour of the program when reading or writing a sequence, this program can do many more things than simply "read and write a sequence".
seqret can read a sequence or many sequences from databases, files, files of sequence names, the command-line or the output of other programs and then can write them to files, the screen or pass them to other programs. Because it can read in a sequence from a database and write it to a file, seqret is a program for extracting sequences from databases. Because it can write the sequence to the screen, seqret is a program for displaying sequences.
seqret can read sequences in any of a wide range of standard sequence formats. You can specify the input and output formats being used. If you don't specify the input format, seqret will try a set of possible formats until it reads it in successfully. Because you can specify the output sequence format, seqret is a program to reformat a sequence.
seqret can read in the reverse complement of a nucleic acid sequence. It therefore is a program for producing the reverse complement of a sequence.
seqret can read in a sequence whose begin and end positions you have specified and write out that fragment. It is therefore a utility for doing simple extraction of a region of a sequence.
seqret can change the case of the sequence being read in to upper or to lower case. It is therefore a simple sequence beautification utility.
seqret can do any combination of the above functions.
The sequence input and output specification of this (and many other EMBOSS programs) is described as being a Uniform Sequence Address.
The Uniform Sequence Address, or USA, is a somewhat tongue-in-cheek reference to a URL-style sequence naming used by all EMBOSS applications.
The USA is a very flexible way of specifying one or more sequences from a variety of sources and includes sequence files, database queries and external applications.
See the full specification of USA syntax at:
http://emboss.sourceforge.net/docs/themes/UniformSequenceAddress.html
The basic USA syntax is one of:
- "file"
- "file:entry"
- "format::file"
- "format::file:entry"
- "database:entry"
- "database"
- "@file"
Note that ':' separates the name of a file containing many possible entries from the specific name of a sequence entry in that file. It also separates the name of a database from an entry in that database
Note also that '::' separates the specified format of a file from the name of the file. Normally the format can be omitted, in which case the program will attempt to identify the correct format when reading the sequence in and will default to using FASTA format when writing the sequence out.
Valid names of the databases set up in your local implementation of EMBOSS can be seen by using the program 'showdb'.
Database queries, and individual entries in files that have more than one sequence entry, use wildcards of "?" for any character and "*" for any string of characters. There are some problems with the Unix shell catching these characters so they do need to be hidden in quotes or preceded by a backslash on the Unix command line, (for example "embl:hs\*")
The output USA name 'stdout' is special. It makes the output go to the device 'standard output'. This is the screen, by default.
Example USAs
The following are valid USAs for sequences:
| USA | Description |
|---|---|
| xxx.seq | A sequence file "xxx.seq" in any format |
| fasta::xxx.seq | A sequence file "xxx.seq" in fasta format |
| gcg::egmsmg.gcg | A sequence file "egmsmg.gcg" in GCG 9 format |
| egmsmg.gcg -sformat=gcg | A sequence file "egmsmg.gcg" in GCG 9 format |
| embl::x13776.em | A sequence file "x13776.em" in EMBL format |
| embl:x13776 | EMBL entry X13776, using whatever access method is defined locally for the EMBL database |
| embl:K01793 | EMBL entry K01793, using whatever access method is defined locally for the EMBL database and searching by accession number and entry name (K01793 is a secondary accession number in this case for entry J01636) |
| embl-acc:K01793 | EMBL entry X13776, using whatever access method is defined locally for the EMBL database and searching by accession number only |
| embl-id:x13776 | EMBL entry x13776, using whatever access method is defined locally for the EMBL database, and searching by ID only |
| embl:v0029* | EMBL entries V00290, V00291, and so on, usually in alphabetical order, using whatever access method is defined locally for the EMBL database |
| embl or EMBL:* | All sequences in the EMBL database |
| @mylist | Reads file mylist and uses each line as a separate USA. This is standard VMS list file syntax, also used in SRS 4.0 but missing in SRS 5.0 onwards. The list file is a list of USAs (one per line). List files can contain references to other lists files or any other standard USA. |
| list::mylist | Same as "@mylist" above |
| 'getz -e [embl-id:x13776] |' | The pipe character "|" causes EMBOSS to fire up getz (SRS) to extract entry x13776 from EMBL in EMBL format. Any application or script which writes one or more sequences to stdout can be used in this way. |
| asis::atacgcagttatctgaccat | So far the shortest USA we could invent. In 'asis' format the name is the sequence so no file needs to be opened. This is a special case. It was intended as a joke, but has proved quite useful for generating command lines when testing. |
Input sequence formats
The input is a standard EMBOSS sequence query (also known as a 'USA').
Major sequence database sources defined as standard in EMBOSS installations include srs:embl, srs:uniprot and ensembl
Data can also be read from sequence output in any supported format written by an EMBOSS or third-party application.
The input format can be specified by using the command-line qualifier -sformat xxx, where 'xxx' is replaced by the name of the required format. The available format names are: gff (gff3), gff2, embl (em), genbank (gb, refseq), ddbj, refseqp, pir (nbrf), swissprot (swiss, sw), dasgff and debug.
See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further information on sequence formats.
Output sequence formats
The output is a standard EMBOSS sequence file.
The results can be output in one of several styles by using the command-line qualifier -osformat xxx, where 'xxx' is replaced by the name of the required format. The available format names are: embl, genbank, gff, pir, swiss, dasgff, debug, listfile, dbmotif, diffseq, excel, feattable, motif, nametable, regions, seqtable, simple, srs, table, tagseq.
See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further information on sequence formats.
Future directions
More formats, both for input and for output, can be easily added, so suggestions are always welcome.Associated qualifiers
As noted previously there are many 'associated' qualifiers that alter the behaviour of seqret when it reads in or writes out a sequence. As these are used in all EMBOSS programs that read in or write out sequences, they are not reported by the '-help' qualifier. They are however reported by the pair of qualifiers: '-help -verbose':
Some of the more useful associated qualifiers are:
| Qualifier | Description |
|---|---|
| -sbegin | The first position to be used in the sequence |
| -send | The last position to be used in the sequence |
| -sreverse | Use the reverse complement of a nucleic acid sequence |
| -sask | Ask the user for begin/end/reverse information |
| -slower | Convert the sequence to lower case |
| -supper | Convert the sequence to upper case |
| -sformat | Specify the input sequence format |
| -osformat | Specify the output sequence format |
| -ossingle | Write each entry into a separate file |
The set of associated qualifiers for sequences behave in different ways depending on where they appear.
If these qualifiers immediately follow a parameter they apply only to that parameter and not to all cases. If they occur before any parameters, they apply to all following sequence parameters.
If there are no two parameters of equal type, the order of parameters and their qualifiers is irrelevant.
Where a qualifier is defined more than once, for example "-sformat" for 2 input sequences to be aligned, the qualifier name can have a number to indicate which sequence is meant. "-sbegin2=25" will apply only to the second sequence, no matter where it appears on the command line.
The -sbegin and -send qualifiers take an integer number specifying the position to begin or end reading a sequence. If the number is positive, the number is the position counting from the first base or residue of the sequence. If the number is negative the position is counted from the end of the sequence, so position -1 is the last base or residue of the sequence. (If -sbegin 0 is used, it is assumed to be the same as -sbegin 1 and -send 0 is the same as -send -1.)
The filter qualifier makes the program behave like a filter, reading its (first) input 'file' from the standard input, and writing its (first) output 'file' to the standard output. The -filter qualifier will also invoke the -auto qualifier, so the user is never prompted for any missing values.
Example:
% cat sequence.seq | seqret -filter | lpr
The example shows the application seqret being run with the -filter qualifier. The input file is 'piped' into the program using the unix command cat and the output is 'piped' directly to the unix program lpr, which will print it on the printer.
When the -options qualifier is used and not all the parameters are given on the command line, it will query the user for those parameters. It will not only query the user for the required parameters as it would do without the -options qualifier, but it will also query the user for the optional parameters.
When the -stdout qualifier is used, the user will still be prompted for all the info that is required, but will write to standard output by default. The user will also still be prompted for an output filename, in case the user wants to save the output to a file.
References
None.Warnings
None.Diagnostic Error Messages
None.Exit status
It always exits with a status of 0.Known bugs
None.See also
| Program name | Description |
|---|---|
| aligncopy | Read and write alignments |
| aligncopypair | Read and write pairs from alignments |
| biosed | Replace or delete sequence sections |
| codcopy | Copy and reformat a codon usage table |
| cutseq | Remove a section from a sequence |
| degapseq | Remove non-alphabetic (e.g. gap) characters from sequences |
| descseq | Alter the name or description of a sequence |
| entret | Retrieve sequence entries from flatfile databases and files |
| extractalign | Extract regions from a sequence alignment |
| extractfeat | Extract features from sequence(s) |
| extractseq | Extract regions from a sequence |
| featcopy | Read and write a feature table |
| featmerge | Merge two overlapping feature tables |
| featreport | Read and write a feature table |
| feattext | Return a feature table original text |
| listor | Write a list file of the logical OR of two sets of sequences |
| makenucseq | Create random nucleotide sequences |
| makeprotseq | Create random protein sequences |
| maskambignuc | Mask all ambiguity characters in nucleotide sequences with N |
| maskambigprot | Mask all ambiguity characters in protein sequences with X |
| maskfeat | Write a sequence with masked features |
| maskseq | Write a sequence with masked regions |
| newseq | Create a sequence file from a typed-in sequence |
| nohtml | Remove mark-up (e.g. HTML tags) from an ASCII text file |
| noreturn | Remove carriage return from ASCII files |
| nospace | Remove whitespace from an ASCII text file |
| notab | Replace tabs with spaces in an ASCII text file |
| notseq | Write to file a subset of an input stream of sequences |
| nthseq | Write to file a single sequence from an input stream of sequences |
| nthseqset | Read and write (return) one set of sequences from many |
| pasteseq | Insert one sequence into another |
| revseq | Reverse and complement a nucleotide sequence |
| seqcount | Read and count sequences |
| seqretsetall | Read and write (return) many sets of sequences |
| seqretsplit | Read sequences and write them to individual files |
| sizeseq | Sort sequences by size |
| skipredundant | Remove redundant sequences from an input set |
| skipseq | Read and write (return) sequences, skipping first few |
| splitsource | Split sequence(s) into original source sequences |
| splitter | Split sequence(s) into smaller sequences |
| trimest | Remove poly-A tails from nucleotide sequences |
| trimseq | Remove unwanted characters from start and end of sequence(s) |
| trimspace | Remove extra whitespace from an ASCII text file |
| union | Concatenate multiple sequences into a single sequence |
| vectorstrip | Remove vectors from the ends of nucleotide sequence(s) |
| yank | Add a sequence reference (a full USA) to a list file |
Valid names of the databases set up in your local implementation of EMBOSS can be seen by using the program 'showdb'.
Author(s)
Peter RiceEuropean Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.
History
1999 - Written by Peter RiceFeb 2002 - '-feature' qualifier added by Peter Rice
Target users
This program is intended to be used by everyone and everything, from naive users to embedded scripts.Comments
Fasta output format
Question
When i tried to convert the EMBL format file into fasta format using the program "seqret", I found that the Access.no appears twice...
>AF102796 AF102796 Homo sapiens alphaE-catenin (CTNNA1) gene, exon 11.
Answer
"It is not a bug ... it is a feature"There are many "FASTA formats". EMBOSS uses the format that ACEDB and the EBI genome projects use. The first field after the ID is the accession number, so that accession numbers can be kept when sequences are converted to FASTA format, without using the NCBI format (with '|' characters in the IDs).
Your EMBL format file has IDs that look like accession numbers, so EMBOSS fills in the accession number for each sequence, and reports it in the FASTA format.