extractfeat Wiki The master copies of EMBOSS documentation are available at http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki. Please help by correcting and extending the Wiki pages. Function Extract features from sequence(s) Description extractfeat is a simple utility for extracting regions of a sequence that are annotated as being a specified type of feature. It reads one or more sequences, and writes out the sequences and features of interest to an output sequence file. 'joined' features can either be extracted as individual sequences, or as a single concatenated sequence if the -join qualifier is used. If the feature is annotated as being in the reverse sense of a nucleic acid sequence, then that feature's sub-sequence is reverse-complemented before it is written. There are many options control exactly what parts of the feature table are given in the output file. In addition, it is often useful to have contextual information about a feature. There are options to specify a number of positions before and/or after the specified feature which will be reported in the output file. Usage Here is a sample session with extractfeat To write out the exons of a sequence: % extractfeat tembl:x65921 -type exon Extract features from sequence(s) output sequence [x65921.fasta]: Go to the input files for this example Go to the output files for this example Example 2 To write out the exons with 10 extra bases at the start and end so that you can inspect the splice sites: % extractfeat tembl:x65921 -type exon -before 10 -after 10 Extract features from sequence(s) output sequence [x65921.fasta]: Go to the output files for this example Example 3 To write out the 10 bases around the start of all 'exon' features in the tembl database: % extractfeat "tembl:*" -type exon -before 5 -after -5 Extract features from sequence(s) output sequence [h45989.fasta]: Go to the output files for this example Example 4 To extract the CDS region with the exons joined into one sequence: % extractfeat tembl:x65921 -type CDS -join Extract features from sequence(s) output sequence [x65921.fasta]: Go to the output files for this example Example 5 To write out the 7 residues around all phosphorylated serine residues % extractfeat "tsw:*" -type MOD_RES -value "phosphoserine*" -before 3 -after -4 Extract features from sequence(s) output sequence [12s1_arath.fasta]: ajSeqxrefNewDbS '1-I' 'FT025' Go to the output files for this example Command line arguments Extract features from sequence(s) Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers: [-sequence] seqall Sequence(s) filename and optional format, or reference (input USA) [-outseq] seqout [.] Sequence filename and optional format (output USA) Additional (Optional) qualifiers: -before integer [0] If this value is greater than 0 then that number of bases or residues before the feature are included in the extracted sequence. This allows you to get the context of the feature. If this value is negative then the start of the extracted sequence will be this number of bases/residues before the end of the feature. So a value of '10' will start the extraction 10 bases/residues before the start of the sequence, and a value of '-10' will start the extraction 10 bases/residues before the end of the feature. The output sequence will be padded with 'N' or 'X' characters if the sequence starts after the required start of the extraction. (Any integer value) -after integer [0] If this value is greater than 0 then that number of bases or residues after the feature are included in the extracted sequence. This allows you to get the context of the feature. If this value is negative then the end of the extracted sequence will be this number of bases/residues after the start of the feature. So a value of '10' will end the extraction 10 bases/residues after the end of the sequence, and a value of '-10' will end the extraction 10 bases/residues after the start of the feature. The output sequence will be padded with 'N' or 'X' characters if the sequence ends before the required end of the extraction. (Any integer value) -source string [*] By default any feature source in the feature table is shown. You can set this to match any feature source you wish to show. The source name is usually either the name of the program that detected the feature or it is the feature table (eg: EMBL) that the feature came from. The source may be wildcarded by using '*'. If you wish to show more than one source, separate their names with the character '|', eg: gene* | embl (Any string) -type string [*] By default every feature in the feature table is extracted. You can set this to be any feature type you wish to extract. See http://www.ebi.ac.uk/embl/WebFeat/ for a list of the EMBL feature types and see the Uniprot user manual in http://www.uniprot.org/manual/sequence_annotat ion for a list of the Uniprot feature types. The type may be wildcarded by using '*'. If you wish to extract more than one type, separate their names with the character '|', eg: *UTR | intron (Any string) -sense integer [0 - any sense, 1 - forward sense, -1 - reverse sense] By default any feature type in the feature table is extracted. You can set this to match any feature sense you wish. 0 - any sense, 1 - forward sense, -1 - reverse sense (Any integer value) -minscore float [0.0] Minimum score of feature to extract (see also maxscore) (Any numeric value) -maxscore float [0.0] Maximum score of feature to extract. If both minscore and maxscore are zero (the default), then any score is ignored (Any numeric value) -tag string [*] Tags are the types of extra values that a feature may have. For example in the EMBL feature table, a 'CDS' type of feature may have the tags '/codon', '/codon_start', '/db_xref', '/EC_number', '/evidence', '/exception', '/function', '/gene', '/label', '/map', '/note', '/number', '/partial', '/product', '/protein_id', '/pseudo', '/standard_name', '/translation', '/transl_except', '/transl_table', or '/usedin'. Some of these tags also have values, for example '/gene' can have the value of the gene name. By default any feature tag in the feature table is extracted. You can set this to match any feature tag you wish to show. The tag may be wildcarded by using '*'. If you wish to extract more than one tag, separate their names with the character '|', eg: gene | label (Any string) -value string [*] Tag values are the values associated with a feature tag. Tags are the types of extra values that a feature may have. For example in the EMBL feature table, a 'CDS' type of feature may have the tags '/codon', '/codon_start', '/db_xref', '/EC_number', '/evidence', '/exception', '/function', '/gene', '/label', '/map', '/note', '/number', '/partial', '/product', '/protein_id', '/pseudo', '/standard_name', '/translation', '/transl_except', '/transl_table', or '/usedin'. Only some of these tags can have values, for example '/gene' can have the value of the gene name. By default any feature tag value in the feature table is shown. You can set this to match any feature tag value you wish to show. The tag value may be wildcarded by using '*'. If you wish to show more than one tag value, separate their names with a space or the character '|', eg: pax* | 10 (Any string) -join boolean [N] Some features, such as CDS (coding sequence) and mRNA are composed of introns concatenated together. There may be other forms of 'joined' sequence, depending on the feature table. If this option is set TRUE, then any group of these features will be output as a single sequence. If the 'before' and 'after' qualifiers have been set, then only the sequence before the first feature and after the last feature are added. -featinname boolean [N] To aid you in identifying the type of feature that has been output, the type of feature is added to the start of the description of the output sequence. Sometimes the description of a sequence is lost in subsequent processing of the sequences file, so it is useful for the type to be a part of the sequence ID name. If you set this to be TRUE then the name is added to the ID name of the output sequence. -describe string To aid you in identifying some further properties of a feature that has been output, this lets you specify one or more tag names that should be added to the output sequence Description text, together with their values (if any). For example, if this is set to be 'gene', then if any output feature has the tag (for example) '/gene=BRCA1' associated with it, then the text '(gene=BRCA1)' will be added to the Description line. Tags are the types of extra values that a feature may have. For example in the EMBL feature table, a 'CDS' type of feature may have the tags '/codon', '/codon_start', '/db_xref', '/EC_number', '/evidence', '/exception', '/function', '/gene', '/label', '/map', '/note', '/number', '/partial', '/product', '/protein_id', '/pseudo', '/standard_name', '/translation', '/transl_except', '/transl_table', or '/usedin'. Some of these tags also have values, for example '/gene' can have the value of the gene name. By default no feature tag is displayed. You can set this to match any feature tag you wish to show. The tag may be wildcarded by using '*'. If you wish to extract more than one tag, separate their names with the character '|', eg: gene | label (Any string) Advanced (Unprompted) qualifiers: (none) Associated qualifiers: "-sequence" associated qualifiers -sbegin1 integer Start of each sequence to be used -send1 integer End of each sequence to be used -sreverse1 boolean Reverse (if DNA) -sask1 boolean Ask for begin/end/reverse -snucleotide1 boolean Sequence is nucleotide -sprotein1 boolean Sequence is protein -slower1 boolean Make lower case -supper1 boolean Make upper case -sformat1 string Input sequence format -sdbname1 string Database name -sid1 string Entryname -ufo1 string UFO features -fformat1 string Features format -fopenfile1 string Features file name "-outseq" associated qualifiers -osformat2 string Output seq format -osextension2 string File name extension -osname2 string Base file name -osdirectory2 string Output directory -osdbname2 string Database name to add -ossingle2 boolean Separate file for each entry -oufo2 string UFO features -offormat2 string Features format -ofname2 string Features file name -ofdirectory2 string Output directory General qualifiers: -auto boolean Turn off prompts -stdout boolean Write first file to standard output -filter boolean Read first file from standard input, write first file to standard output -options boolean Prompt for standard and additional values -debug boolean Write debug output to program.dbg -verbose boolean Report some/full command line options -help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose -warning boolean Report warnings -error boolean Report errors -fatal boolean Report fatal errors -die boolean Report dying program messages -version boolean Report version number and exit Input file format extractfeat reads normal sequences with features. Feature tables in Swissprot, EMBL, GFF, etc. format can be added using '-ufo featurefile' on the command line. Input files for usage example 'tembl:x65921' is a sequence entry in the example nucleic acid database 'tembl' Database entry: tembl:x65921 ID X65921; SV 1; linear; genomic DNA; STD; HUM; 2016 BP. XX AC X65921; S45242; XX DT 13-MAY-1992 (Rel. 31, Created) DT 14-NOV-2006 (Rel. 89, Last updated, Version 7) XX DE H.sapiens fau 1 gene XX KW fau 1 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 1-2016 RA Kas K.; RT ; RL Submitted (29-APR-1992) to the EMBL/GenBank/DDBJ databases. RL K. Kas, University of Antwerp, Dept of Biochemistry T3.22, RL Universiteitsplein 1, 2610 Wilrijk, BELGIUM XX RN [2] RP 1-2016 RX DOI; 10.1016/0006-291X(92)91286-Y. RX PUBMED; 1326960. RA Kas K., Michiels L., Merregaert J.; RT "Genomic structure and expression of the human fau gene: encoding the RT ribosomal protein S30 fused to a ubiquitin-like protein"; RL Biochem. Biophys. Res. Commun. 187(2):927-933(1992). XX DR GDB; 191789. DR GDB; 191790. DR GDB; 354872. DR GDB; 4590236. XX FH Key Location/Qualifiers FH FT source 1..2016 FT /organism="Homo sapiens" FT /mol_type="genomic DNA" FT /clone_lib="CML cosmid" FT /clone="15.1" FT /db_xref="taxon:9606" FT mRNA join(408..504,774..856,951..1095,1557..1612,1787..>1912) FT /gene="fau 1" FT exon 408..504 FT /number=1 [Part of this file has been deleted for brevity] FT RAKRRMQYNRRFVNVVPTFGKKKGPNANS" FT intron 857..950 FT /number=2 FT exon 951..1095 FT /number=3 FT intron 1096..1556 FT /number=3 FT exon 1557..1612 FT /number=4 FT intron 1613..1786 FT /number=4 FT exon 1787..>1912 FT /number=5 FT polyA_signal 1938..1943 XX SQ Sequence 2016 BP; 421 A; 562 C; 538 G; 495 T; 0 other; ctaccatttt ccctctcgat tctatatgta cactcgggac aagttctcct gatcgaaaac 60 ggcaaaacta aggccccaag taggaatgcc ttagttttcg gggttaacaa tgattaacac 120 tgagcctcac acccacgcga tgccctcagc tcctcgctca gcgctctcac caacagccgt 180 agcccgcagc cccgctggac accggttctc catccccgca gcgtagcccg gaacatggta 240 gctgccatct ttacctgcta cgccagcctt ctgtgcgcgc aactgtctgg tcccgccccg 300 tcctgcgcga gctgctgccc aggcaggttc gccggtgcga gcgtaaaggg gcggagctag 360 gactgccttg ggcggtacaa atagcaggga accgcgcggt cgctcagcag tgacgtgaca 420 cgcagcccac ggtctgtact gacgcgccct cgcttcttcc tctttctcga ctccatcttc 480 gcggtagctg ggaccgccgt tcaggtaaga atggggcctt ggctggatcc gaagggcttg 540 tagcaggttg gctgcggggt cagaaggcgc ggggggaacc gaagaacggg gcctgctccg 600 tggccctgct ccagtcccta tccgaactcc ttgggaggca ctggccttcc gcacgtgagc 660 cgccgcgacc accatcccgt cgcgatcgtt tctggaccgc tttccactcc caaatctcct 720 ttatcccaga gcatttcttg gcttctctta caagccgtct tttctttact cagtcgccaa 780 tatgcagctc tttgtccgcg cccaggagct acacaccttc gaggtgaccg gccaggaaac 840 ggtcgcccag atcaaggtaa ggctgcttgg tgcgccctgg gttccatttt cttgtgctct 900 tcactctcgc ggcccgaggg aacgcttacg agccttatct ttccctgtag gctcatgtag 960 cctcactgga gggcattgcc ccggaagatc aagtcgtgct cctggcaggc gcgcccctgg 1020 aggatgaggc cactctgggc cagtgcgggg tggaggccct gactaccctg gaagtagcag 1080 gccgcatgct tggaggtgag tgagagagga atgttctttg aagtaccggt aagcgtctag 1140 tgagtgtggg gtgcatagtc ctgacagctg agtgtcacac ctatggtaat agagtacttc 1200 tcactgtctt cagttcagag tgattcttcc tgtttacatc cctcatgttg aacacagacg 1260 tccatgggag actgagccag agtgtagttg tatttcagtc acatcacgag atcctagtct 1320 ggttatcagc ttccacacta aaaattaggt cagaccaggc cccaaagtgc tctataaatt 1380 agaagctgga agatcctgaa atgaaactta agatttcaag gtcaaatatc tgcaactttg 1440 ttctcattac ctattgggcg cagcttctct ttaaaggctt gaattgagaa aagaggggtt 1500 ctgctgggtg gcaccttctt gctcttacct gctggtgcct tcctttccca ctacaggtaa 1560 agtccatggt tccctggccc gtgctggaaa agtgagaggt cagactccta aggtgagtga 1620 gagtattagt ggtcatggtg ttaggacttt ttttcctttc acagctaaac caagtccctg 1680 ggctcttact cggtttgcct tctccctccc tggagatgag cctgagggaa gggatgctag 1740 gtgtggaaga caggaaccag ggcctgatta accttccctt ctccaggtgg ccaaacagga 1800 gaagaagaag aagaagacag gtcgggctaa gcggcggatg cagtacaacc ggcgctttgt 1860 caacgttgtg cccacctttg gcaagaagaa gggccccaat gccaactctt aagtcttttg 1920 taattctggc tttctctaat aaaaaagcca cttagttcag tcatcgcatt gtttcatctt 1980 tacttgcaag gcctcaggga gaggtgtgct tctcgg 2016 // Output file format Output files for usage example File: x65921.fasta >X65921_408_504 [exon] H.sapiens fau 1 gene cagtgacgtgacacgcagcccacggtctgtactgacgcgccctcgcttcttcctctttct cgactccatcttcgcggtagctgggaccgccgttcag >X65921_774_856 [exon] H.sapiens fau 1 gene tcgccaatatgcagctctttgtccgcgcccaggagctacacaccttcgaggtgaccggcc aggaaacggtcgcccagatcaag >X65921_951_1095 [exon] H.sapiens fau 1 gene gctcatgtagcctcactggagggcattgccccggaagatcaagtcgtgctcctggcaggc gcgcccctggaggatgaggccactctgggccagtgcggggtggaggccctgactaccctg gaagtagcaggccgcatgcttggag >X65921_1557_1612 [exon] H.sapiens fau 1 gene gtaaagtccatggttccctggcccgtgctggaaaagtgagaggtcagactcctaag >X65921_1787_1912 [exon] H.sapiens fau 1 gene gtggccaaacaggagaagaagaagaagaagacaggtcgggctaagcggcggatgcagtac aaccggcgctttgtcaacgttgtgcccacctttggcaagaagaagggccccaatgccaac tcttaa Output files for usage example 2 File: x65921.fasta >X65921_408_504 [exon] H.sapiens fau 1 gene ggtcgctcagcagtgacgtgacacgcagcccacggtctgtactgacgcgccctcgcttct tcctctttctcgactccatcttcgcggtagctgggaccgccgttcaggtaagaatgg >X65921_774_856 [exon] H.sapiens fau 1 gene ctttactcagtcgccaatatgcagctctttgtccgcgcccaggagctacacaccttcgag gtgaccggccaggaaacggtcgcccagatcaaggtaaggctgc >X65921_951_1095 [exon] H.sapiens fau 1 gene ttccctgtaggctcatgtagcctcactggagggcattgccccggaagatcaagtcgtgct cctggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggccct gactaccctggaagtagcaggccgcatgcttggaggtgagtgaga >X65921_1557_1612 [exon] H.sapiens fau 1 gene cccactacaggtaaagtccatggttccctggcccgtgctggaaaagtgagaggtcagact cctaaggtgagtgaga >X65921_1787_1912 [exon] H.sapiens fau 1 gene ccttctccaggtggccaaacaggagaagaagaagaagaagacaggtcgggctaagcggcg gatgcagtacaaccggcgctttgtcaacgttgtgcccacctttggcaagaagaagggccc caatgccaactcttaagtcttttgta Output files for usage example 3 File: h45989.fasta >X65921_408_504 [exon] H.sapiens fau 1 gene ctcagcagtg >X65921_774_856 [exon] H.sapiens fau 1 gene ctcagtcgcc >X65921_951_1095 [exon] H.sapiens fau 1 gene tgtaggctca >X65921_1557_1612 [exon] H.sapiens fau 1 gene tacaggtaaa >X65921_1787_1912 [exon] H.sapiens fau 1 gene tccaggtggc >K00650_889_1029 [exon] Human fos proto-oncogene (c-fos), complete cds. ccacgatgat >K00650_1783_2034 [exon] Human fos proto-oncogene (c-fos), complete cds. tctaggactt >K00650_2466_2573 [exon] Human fos proto-oncogene (c-fos), complete cds. tctagttatc >K00650_2688_3329 [exon] Human fos proto-oncogene (c-fos), complete cds. tacaggagac >D00596_1001_1205 [exon] Homo sapiens gene for thymidylate synthase, complete cd s. gcgccatgcc >D00596_2895_2968 [exon] Homo sapiens gene for thymidylate synthase, complete cd s. ttcagatgaa >D00596_5396_5570 [exon] Homo sapiens gene for thymidylate synthase, complete cd s. tccagggatc >D00596_11843_11944 [exon] Homo sapiens gene for thymidylate synthase, complete cds. tacagattat >D00596_13449_13624 [exon] Homo sapiens gene for thymidylate synthase, complete cds. ctcagatctt >D00596_14133_14204 [exon] Homo sapiens gene for thymidylate synthase, complete cds. tatagccagg >D00596_15613_15750 [exon] Homo sapiens gene for thymidylate synthase, complete cds. tttagcttca >AB009071_67_155 [exon] Homo sapiens HERG gene, complete cds. cccgcccatg >AB009071_356_586 [exon] Homo sapiens HERG gene, complete cds. cctaggccgt >AB009071_768_932 [exon] Homo sapiens HERG gene, complete cds. tgcagggagc >AB009071_1137_1580 [exon] Homo sapiens HERG gene, complete cds. cgcaggccgc >AB009071_1742_1953 [exon] Homo sapiens HERG gene, complete cds. cctaggggcc >AB009071_2168_2596 [exon] Homo sapiens HERG gene, complete cds. tgcaggtcct >AB009071_2765_3152 [exon] Homo sapiens HERG gene, complete cds. cccagctgat >AB009071_3332_3531 [exon] Homo sapiens HERG gene, complete cds. cccagccctc >AB009071_3716_3968 [exon] Homo sapiens HERG gene, complete cds. cccaggtgct [Part of this file has been deleted for brevity] aacagctcct >U01317_39414_39558 [exon] Human beta globin region on chromosome 11. tccacacact >U01317_39681_39903 [exon] Human beta globin region on chromosome 11. cacaggctcc >U01317_40770_40985 [exon] Human beta globin region on chromosome 11. aacagctcct >U01317_45710_45800 [exon] Human beta globin region on chromosome 11. acactgtagt >U01317_45922_46145 [exon] Human beta globin region on chromosome 11. cacagtctcc >U01317_46997_47124 [exon] Human beta globin region on chromosome 11. cccagctctt >U01317_54740_54881 [exon] Human beta globin region on chromosome 11. tgcttacact >U01317_55010_55232 [exon] Human beta globin region on chromosome 11. ctcagattac >U01317_56131_56389 [exon] Human beta globin region on chromosome 11. cgcagctctt >U01317_62137_62278 [exon] Human beta globin region on chromosome 11. tgcttacatt >U01317_62187_62278 [exon] Human beta globin region on chromosome 11. acaccatggt >U01317_62390_62408 [exon] Human beta globin region on chromosome 11. attggtctat >U01317_62409_62631 [exon] Human beta globin region on chromosome 11. cttaggctgc >U01317_63482_63742 [exon] Human beta globin region on chromosome 11. cacagctcct >M23100_1541_1923 [exon] Human insulin receptor (INSR) gene, exon 1, clones lamb da-hINSR-(1-13). ctccgggccc >M23100_1542_1923 [exon] Human insulin receptor (INSR) gene, exon 1, clones lamb da-hINSR-(1-13). tccgggcccc >M23100_1548_1923 [exon] Human insulin receptor (INSR) gene, exon 1, clones lamb da-hINSR-(1-13). ccccgagatc >V00451_363_460 [exon] Glycine max leghemoglobin gene or pseudogene (no mRNA det ected). gaaatatggg >V00451_555_663 [exon] Glycine max leghemoglobin gene or pseudogene (no mRNA det ected). aataggatat >V00451_2182_2286 [exon] Glycine max leghemoglobin gene or pseudogene (no mRNA d etected). tgtaggtgcg >V00451_3065_3208 [exon] Glycine max leghemoglobin gene or pseudogene (no mRNA d etected). cgtaggtggt >M11903_351_499 [exon] Rattus norvegicus androgen-responsive protein precursor ( Svf) gene, exons 1 and 1A, alternatively spliced. cctgtaggca >M11903_401_499 [exon] Rattus norvegicus androgen-responsive protein precursor ( Svf) gene, exons 1 and 1A, alternatively spliced. gctctcagtc >M11904_109_445 [exon] Rattus norvegicus androgen-responsive protein precursor ( Svf) gene, exon 2 and complete cds. aacagaaaaa >M11905_233_420 [exon] Rattus norvegicus androgen-responsive protein precursor ( Svf) gene, exon 3. cacaggttgt Output files for usage example 4 File: x65921.fasta >X65921_782_1912 [CDS] H.sapiens fau 1 gene atgcagctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacg gtcgcccagatcaaggctcatgtagcctcactggagggcattgccccggaagatcaagtc gtgctcctggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggag gccctgactaccctggaagtagcaggccgcatgcttggaggtaaagtccatggttccctg gcccgtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaag aagaagacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtg cccacctttggcaagaagaagggccccaatgccaactcttaa Output files for usage example 5 File: 12s1_arath.fasta >AQP1_HUMAN_247_247 [protein_modification_categorized_by_chemical_process] Aquap orin-1 (AQP-1) (Aquaporin-CHIP) (Water channel protein for red blood cells and k idney proximal tubule) (Urine water channel) VWTSGQV >AQP1_HUMAN_262_262 [protein_modification_categorized_by_chemical_process] Aquap orin-1 (AQP-1) (Aquaporin-CHIP) (Water channel protein for red blood cells and k idney proximal tubule) (Urine water channel) DINSRVE >GCN4_YEAST_17_17 [protein_modification_categorized_by_chemical_process] General control protein GCN4 (Amino acid biosynthesis regulatory protein) MGFSPLD >GCN4_YEAST_218_218 [protein_modification_categorized_by_chemical_process] Gener al control protein GCN4 (Amino acid biosynthesis regulatory protein) IPLSPIV >OPSD_HUMAN_334_334 [protein_modification_categorized_by_chemical_process] Rhodo psin (Opsin-2) DEASATV >OPSD_HUMAN_338_338 [protein_modification_categorized_by_chemical_process] Rhodo psin (Opsin-2) ATVSKTE >OPSD_HUMAN_343_343 [protein_modification_categorized_by_chemical_process] Rhodo psin (Opsin-2) TETSQVA >PAXI_HUMAN_83_83 [protein_modification_categorized_by_chemical_process] Paxilli n QPQSSSP >PAXI_HUMAN_85_85 [protein_modification_categorized_by_chemical_process] Paxilli n QSSSPVY >PAXI_HUMAN_106_106 [protein_modification_categorized_by_chemical_process] Paxil lin SVGSPCS >PAXI_HUMAN_109_109 [protein_modification_categorized_by_chemical_process] Paxil lin SPCSRVG >PAXI_HUMAN_126_126 [protein_modification_categorized_by_chemical_process] Paxil lin KQKSAEP >PAXI_HUMAN_130_130 [protein_modification_categorized_by_chemical_process] Paxil lin AEPSPTV >PAXI_HUMAN_137_137 [protein_modification_categorized_by_chemical_process] Paxil lin MSTSLGS >PAXI_HUMAN_303_303 [protein_modification_categorized_by_chemical_process] Paxil lin GRSSPGG >UBR5_RAT_193_193 [protein_modification_categorized_by_chemical_process] E3 ubiq uitin-protein ligase UBR5 (6.3.2.-) (E3 ubiquitin-protein ligase, HECT domain-co ntaining 1) (Hyperplastic discs protein homolog) (100 kDa protein) (Fragment) GRPSQGL >UBR5_RAT_607_607 [protein_modification_categorized_by_chemical_process] E3 ubiq uitin-protein ligase UBR5 (6.3.2.-) (E3 ubiquitin-protein ligase, HECT domain-co ntaining 1) (Hyperplastic discs protein homolog) (100 kDa protein) (Fragment) SSRSVVD The sequences of the specified features are written out. The ID name of the sequence is formed from the original sequence name with the start and end positions of the feature appended to it. So if the feature came from a sequence with an ID name of 'XYZ' from positions 10 to 22, then the resulting ID name of the feature sequence will be 'XYZ_10_22' The name of the type of feature is added to the start of the description of the sequence in brackets, e.g.: '[exon]'. The sequence is written out as a normal sequence. If the feature is in the reverse sense of a nucleic acid sequence, then it is reverse-complemented before being written. Data files None. Notes Bear in mind that database annotation cannot always be trusted to be reliable. If you rely upon annotation written by other people or another program and do not independently verify such annotation, then there is a chance that some of the reported features will be erreneous. Controlling the output There are many options to control exactly what parts of the feature table are written to file. By default every feature in the feature table is extracted. -type will set the specific feature type to extract. See http://www.ebi.ac.uk/embl/WebFeindex.html for a list of the EMBL feature types and see Appendix A of the Swissprot user manual in http://www.uniprot.org/manual/sequence_annotation for a list of the Swissprot feature types. By default any feature tag in the feature table is extracted. -tag specifies a feature tag reuired in any feature extracted. Tags are the types of extra values that a feature may have. For example in the EMBL feature table, a 'CDS' type of feature may have the tags /codon, /codon_start, /db_xref, /EC_number, /evidence, /exception, /function, /gene, /label, /map, /note, /number, /partial, /product, /protein_id,/pseudo, /standard_name, /translation, /transl_except, /transl_table, or /usedin. Some of these tags also have values, for example /gene can have the value of the gene name. By default any feature tag value in the feature table is shown. You can set this using -tag to match any specific feature tag value you wish to show. Tag values are the values associated with a feature tag, for example /gene can have the value of the gene name. Bear in mind only some of these tags can have values. By default any feature source in the feature table is shown. -source is used to set this to match a specific feature source. By default features in either sense are extracted. The -sense option specifies a particular sense. The minimum and maximum score of features to be reported may be specified with -minscore and -maxscore. To aid you in identifying the type of feature that has been output, the type of feature is added to the start of the description of the output sequence. Sometimes the description of a sequence is lost in subsequent processing of the sequences file, so it is useful for the type to be a part of the output sequence ID name. The -featinname option specifies this behaviour. To aid you in identifying the properties of a feature that has been output, -describe specifies one or more tag names that will be added to the output sequence "Description" text, together with their values (if any). For example, if this is set to be gene, then if any output feature has the tag (for example) /gene=BRCA1 associated with it, then the text (gene=BRCA1) will be added to the Description line. By default no feature tag is given in the "Description" text. You can set -describe to specify any feature tag you wish to show. "Joined" features Some features, such as CDS (coding sequence) and mRNA are composed of introns concatenated together. There may be other forms of 'joined' sequence, depending on the feature table. By default, 'joined' features are extracted as individual sequences. If the -join option is specified, then any group of these features will be output as a single sequence. If the -before and -after qualifiers have been set, then only the sequence before the first feature and after the last feature are added. References None. Warnings Diagnostic Error Messages If the end position of the sequence to be written is less than the start position, then the warning message "Extraction region end less than start for feature type [start-end] in ID name" is written and no sequence is output. Exit status It always exits with status 0. Known bugs None. See also Program name Description aligncopy Reads and writes alignments aligncopypair Reads and writes pairs from alignments biosed Replace or delete sequence sections codcopy Copy and reformat a codon usage table cutseq Removes a section from a sequence degapseq Removes non-alphabetic (e.g. gap) characters from sequences descseq Alter the name or description of a sequence entret Retrieves sequence entries from flatfile databases and files extractalign Extract regions from a sequence alignment extractseq Extract regions from a sequence featcopy Reads and writes a feature table featreport Reads and writes 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 Masks all ambiguity characters in nucleotide sequences with N maskambigprot Masks 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 Reads and writes (returns) one set of sequences from many pasteseq Insert one sequence into another revseq Reverse and complement a nucleotide sequence seqcount Reads and counts sequences seqret Reads and writes (returns) sequences seqretsetall Reads and writes (returns) many sets of sequences seqretsplit Reads sequences and writes them to individual files showfeat Display features of a sequence in pretty format sizeseq Sort sequences by size skipredundant Remove redundant sequences from an input set skipseq Reads and writes (returns) 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 twofeat Finds neighbouring pairs of features in sequence(s) union Concatenate multiple sequences into a single sequence vectorstrip Removes vectors from the ends of nucleotide sequence(s) yank Add a sequence reference (a full USA) to a list file Author(s) Gary Williams formerly at: MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK Please report all bugs to the EMBOSS bug team (emboss-bug (c) emboss.open-bio.org) not to the original author. History Written (Dec 12 2001) - Gary Williams Added '-join' parameter (June 2002) - Gary Williams Target users This program is intended to be used by everyone and everything, from naive users to embedded scripts. Comments None