yank |
In fact, it writes out not just the name of the sequence, but also the start and end position of a region within that sequence and, if the sequence is nucleic, if can specify whether the sequence is the reverse complement.
Without the program yank you would need to use a text editor such as pico to create the appropriate list files. yank makes this process easy.
Instead of containing the sequences themselves, a List file contains "references" to sequences - so, for example, you might include database entries, the names of files containing sequences, or even the names of other list files. For example, here's a valid list file, called seq.list:
unix % more seq.list opsd_abyko.fasta sw:opsd_xenla sw:opsd_c* @another_list
This looks a bit odd, but it's really very straightforward; the file contains:
Notice the @ in front of the last entry. This is the way you tell EMBOSS that this file is a list file, not a regular sequence file.
This is an example of adding an entry for the part of tembl:hsfau1 between positions 1913 and 1915 to the existing list file 'cds.list':
% yank Reads a sequence range, appends the full USA to a list file Input sequence: tembl:hsfau1 Begin at position [start]: 1913 End at position [end]: 1915 Reverse strand [N]: Output file [hsfau1.yank]: cds.list |
Go to the input files for this example
Go to the output files for this example
Standard (Mandatory) qualifiers: [-sequence] sequence Sequence USA [-outfile] outfile Output file name Additional (Optional) qualifiers: (none) Advanced (Unprompted) qualifiers: -newfile boolean Overwrite existing output file Associated qualifiers: "-sequence" associated qualifiers -sbegin1 integer Start of the sequence to be used -send1 integer End of the 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 "-outfile" associated qualifiers -odirectory2 string Output directory General qualifiers: -auto boolean Turn off prompts -stdout boolean Write standard output -filter boolean Read standard input, write 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. 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 deaths |
Standard (Mandatory) qualifiers | Allowed values | Default | |
---|---|---|---|
[-sequence] (Parameter 1) |
Sequence USA | Readable sequence | Required |
[-outfile] (Parameter 2) |
Output file name | Output file | <sequence>.yank |
Additional (Optional) qualifiers | Allowed values | Default | |
(none) | |||
Advanced (Unprompted) qualifiers | Allowed values | Default | |
-newfile | Overwrite existing output file | Boolean value Yes/No | No |
You will be prompted for the start and end positions you wish to use.
If the sequence is nucleic, you will be prompted whether you wish to use the reverse complement of the sequence.
ID HSFAU1 standard; DNA; HUM; 2016 BP. XX AC X65921; S45242; XX SV X65921.1 XX DT 13-MAY-1992 (Rel. 31, Created) DT 21-JUL-1993 (Rel. 36, Last updated, Version 5) 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; Primates; Catarrhini; Hominidae; 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 MEDLINE; 92412144. 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. 187:927-933(1992). XX DR SWISS-PROT; P35544; UBIM_HUMAN. DR SWISS-PROT; Q05472; RS30_HUMAN. XX FH Key Location/Qualifiers FH FT source 1..2016 FT /db_xref="taxon:9606" FT /organism="Homo sapiens" FT /clone_lib="CML cosmid" FT /clone="15.1" FT mRNA join(408..504,774..856,951..1095,1557..1612,1787..>1912) FT /gene="fau 1" FT exon 408..504 FT /number=1 FT intron 505..773 FT /number=1 FT exon 774..856 [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 // |
tembl-id:HSFAU1[782:856] tembl-id:HSFAU1[951:1095] tembl-id:HSFAU1[1557:1612] tembl-id:HSFAU1[1787:1912] tembl-id:HSFAU1[1913:1915] |
The output list file can now be read in by a program such as union by specifying the list file as '@cds.list' when union prompts for input.
Program name | Description |
---|---|
biosed | Replace or delete sequence sections |
codcopy | Reads and writes a codon usage table |
cutseq | Removes a specified section from a sequence |
degapseq | Removes gap characters from sequences |
descseq | Alter the name or description of a sequence |
entret | Reads and writes (returns) flatfile entries |
extractfeat | Extract features from a sequence |
extractseq | Extract regions from a sequence |
listor | Write a list file of the logical OR of two sets of sequences |
maskfeat | Mask off features of a sequence |
maskseq | Mask off regions of a sequence |
newseq | Type in a short new sequence |
noreturn | Removes carriage return from ASCII files |
notseq | Exclude a set of sequences and write out the remaining ones |
nthseq | Writes one sequence from a multiple set of sequences |
pasteseq | Insert one sequence into another |
revseq | Reverse and complement a sequence |
seqret | Reads and writes (returns) sequences |
seqretsplit | Reads and writes (returns) sequences in individual files |
skipseq | Reads and writes (returns) sequences, skipping first few |
splitter | Split a sequence into (overlapping) smaller sequences |
trimest | Trim poly-A tails off EST sequences |
trimseq | Trim ambiguous bits off the ends of sequences |
union | Reads sequence fragments and builds one sequence |
vectorstrip | Strips out DNA between a pair of vector sequences |
The program extract does not make list files, but creates a sequence from sub-regions of a single other sequence.