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sizeseq |
% sizeseq -osformat swiss Sort sequences by size Input sequence set: globins.fasta Return longest sequence first [N]: output sequence(s) [globins.swiss]: |
Go to the input files for this example
Go to the output files for this example
Standard (Mandatory) qualifiers:
[-sequences] seqset Sequence set filename and optional format,
or reference (input USA)
-descending boolean [N] By default the shortest sequence is
given first.
[-outseq] seqoutall [
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| Standard (Mandatory) qualifiers | Allowed values | Default | |
|---|---|---|---|
| [-sequences] (Parameter 1) |
Sequence set filename and optional format, or reference (input USA) | Readable set of sequences | Required |
| -descending | By default the shortest sequence is given first. | Boolean value Yes/No | No |
| [-outseq] (Parameter 2) |
Sequence set(s) filename and optional format (output USA) | Writeable sequence(s) | <*>.format |
| Additional (Optional) qualifiers | Allowed values | Default | |
| (none) | |||
| Advanced (Unprompted) qualifiers | Allowed values | Default | |
| -feature | Sequence feature information will be retained if this option is set. | Boolean value Yes/No | No |
>HBB_HUMAN Sw:Hbb_Human => HBB_HUMAN VHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKV KAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGK EFTPPVQAAYQKVVAGVANALAHKYH >HBB_HORSE Sw:Hbb_Horse => HBB_HORSE VQLSGEEKAAVLALWDKVNEEEVGGEALGRLLVVYPWTQRFFDSFGDLSNPGAVMGNPKV KAHGKKVLHSFGEGVHHLDNLKGTFAALSELHCDKLHVDPENFRLLGNVLVVVLARHFGK DFTPELQASYQKVVAGVANALAHKYH >HBA_HUMAN Sw:Hba_Human => HBA_HUMAN VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGK KVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPA VHASLDKFLASVSTVLTSKYR >HBA_HORSE Sw:Hba_Horse => HBA_HORSE VLSAADKTNVKAAWSKVGGHAGEYGAEALERMFLGFPTTKTYFPHFDLSHGSAQVKAHGK KVGDALTLAVGHLDDLPGALSNLSDLHAHKLRVDPVNFKLLSHCLLSTLAVHLPNDFTPA VHASLDKFLSSVSTVLTSKYR >MYG_PHYCA Sw:Myg_Phyca => MYG_PHYCA VLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLKTEAEMKASED LKKHGVTVLTALGAILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISEAIIHVLHSRHP GDFGADAQGAMNKALELFRKDIAAKYKELGYQG >GLB5_PETMA Sw:Glb5_Petma => GLB5_PETMA PIVDTGSVAPLSAAEKTKIRSAWAPVYSTYETSGVDILVKFFTSTPAAQEFFPKFKGLTT ADQLKKSADVRWHAERIINAVNDAVASMDDTEKMSMKLRDLSGKHAKSFQVDPQYFKVLA AVIADTVAAGDAGFEKLMSMICILLRSAY >LGB2_LUPLU Sw:Lgb2_Luplu => LGB2_LUPLU GALTESQAALVKSSWEEFNANIPKHTHRFFILVLEIAPAAKDLFSFLKGTSEVPQNNPEL QAHAGKVFKLVYEAAIQLQVTGVVVTDATLKNLGSVHVSKGVADAHFPVVKEAILKTIKE VVGAKWSEELNSAWTIAYDELAIVIKKEMNDAA |
ID HBA_HUMAN Unreviewed; 141 AA.
DE Sw:Hba_Human => HBA_HUMAN
SQ SEQUENCE 141 AA; 15127 MW; 34D13618E62A33C1 CRC64;
VLSPADKTNV KAAWGKVGAH AGEYGAEALE RMFLSFPTTK TYFPHFDLSH GSAQVKGHGK
KVADALTNAV AHVDDMPNAL SALSDLHAHK LRVDPVNFKL LSHCLLVTLA AHLPAEFTPA
VHASLDKFLA SVSTVLTSKY R
//
ID HBA_HORSE Unreviewed; 141 AA.
DE Sw:Hba_Horse => HBA_HORSE
SQ SEQUENCE 141 AA; 15115 MW; 128B9100A4D8457A CRC64;
VLSAADKTNV KAAWSKVGGH AGEYGAEALE RMFLGFPTTK TYFPHFDLSH GSAQVKAHGK
KVGDALTLAV GHLDDLPGAL SNLSDLHAHK LRVDPVNFKL LSHCLLSTLA VHLPNDFTPA
VHASLDKFLS SVSTVLTSKY R
//
ID HBB_HUMAN Unreviewed; 146 AA.
DE Sw:Hbb_Human => HBB_HUMAN
SQ SEQUENCE 146 AA; 15868 MW; EACBC707CFD466A1 CRC64;
VHLTPEEKSA VTALWGKVNV DEVGGEALGR LLVVYPWTQR FFESFGDLST PDAVMGNPKV
KAHGKKVLGA FSDGLAHLDN LKGTFATLSE LHCDKLHVDP ENFRLLGNVL VCVLAHHFGK
EFTPPVQAAY QKVVAGVANA LAHKYH
//
ID HBB_HORSE Unreviewed; 146 AA.
DE Sw:Hbb_Horse => HBB_HORSE
SQ SEQUENCE 146 AA; 16009 MW; 734664793DA642EE CRC64;
VQLSGEEKAA VLALWDKVNE EEVGGEALGR LLVVYPWTQR FFDSFGDLSN PGAVMGNPKV
KAHGKKVLHS FGEGVHHLDN LKGTFAALSE LHCDKLHVDP ENFRLLGNVL VVVLARHFGK
DFTPELQASY QKVVAGVANA LAHKYH
//
ID GLB5_PETMA Unreviewed; 149 AA.
DE Sw:Glb5_Petma => GLB5_PETMA
SQ SEQUENCE 149 AA; 16270 MW; CD2305FB92DACD59 CRC64;
PIVDTGSVAP LSAAEKTKIR SAWAPVYSTY ETSGVDILVK FFTSTPAAQE FFPKFKGLTT
ADQLKKSADV RWHAERIINA VNDAVASMDD TEKMSMKLRD LSGKHAKSFQ VDPQYFKVLA
AVIADTVAAG DAGFEKLMSM ICILLRSAY
//
ID MYG_PHYCA Unreviewed; 153 AA.
DE Sw:Myg_Phyca => MYG_PHYCA
SQ SEQUENCE 153 AA; 17200 MW; 543D385C66FEE1E1 CRC64;
VLSEGEWQLV LHVWAKVEAD VAGHGQDILI RLFKSHPETL EKFDRFKHLK TEAEMKASED
LKKHGVTVLT ALGAILKKKG HHEAELKPLA QSHATKHKIP IKYLEFISEA IIHVLHSRHP
GDFGADAQGA MNKALELFRK DIAAKYKELG YQG
//
ID LGB2_LUPLU Unreviewed; 153 AA.
DE Sw:Lgb2_Luplu => LGB2_LUPLU
SQ SEQUENCE 153 AA; 16653 MW; FE29AB9DEF33AFC8 CRC64;
GALTESQAAL VKSSWEEFNA NIPKHTHRFF ILVLEIAPAA KDLFSFLKGT SEVPQNNPEL
QAHAGKVFKL VYEAAIQLQV TGVVVTDATL KNLGSVHVSK GVADAHFPVV KEAILKTIKE
VVGAKWSEEL NSAWTIAYDE LAIVIKKEMN DAA
//
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| 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 |
| extractfeat | Extract features from sequence(s) |
| extractseq | Extract regions from a sequence |
| featcopy | Reads and writes a feature table |
| featreport | Reads and writes a feature table |
| 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 all 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 |
| pasteseq | Insert one sequence into another |
| revseq | Reverse and complement a nucleotide sequence |
| seqret | Reads and writes (returns) sequences |
| seqretsplit | Reads sequences and writes them to individual files |
| skipredundant | Remove redundant sequences from an input set |
| skipseq | Reads and writes (returns) sequences, skipping first few |
| 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 | Removes vectors from the ends of nucleotide sequence(s) |
| yank | Add a sequence reference (a full USA) to a list file |