|
|
seqretsetall |
Please help by correcting and extending the Wiki pages.
% seqretsetall -osf phylip Reads and writes (returns) many sets of sequences Input sequence set(s): globins-all.phy output sequence(s) [globins-all.phylip]: |
Go to the input files for this example
Go to the output files for this example
Standard (Mandatory) qualifiers:
[-sequence] seqsetall Sequence set(s) filename and optional
format, or reference (input USA)
[-outseq] seqoutall [
|
| Standard (Mandatory) qualifiers | Allowed values | Default | |
|---|---|---|---|
| [-sequence] (Parameter 1) |
Sequence set(s) filename and optional format, or reference (input USA) | Readable sets of sequences | Required |
| [-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 | Use feature information | Boolean value Yes/No | No |
7 164
HBB_HUMAN --------VH LTPEEKSAVT ALWGKVN-VD EVGGEALGR- LLVVYPWTQR
HBB_HORSE --------VQ LSGEEKAAVL ALWDKVN-EE EVGGEALGR- LLVVYPWTQR
HBA_HUMAN ---------- ----VLSPAD KTNVKAA-WG KVGAHAGEYG AEALERMFLS
HBA_HORSE ---------- ----VLSAAD KTNVKAA-WS KVGGHAGEYG AEALERMFLG
MYG_PHYCA -------VLS EGEWQLVLHV WAKVEAD-VA GHGQDILIR- LFKSHPETLE
GLB5_PETMAPIVDTGSVAP LSAAEKTKIR SAWAPVYSTY ETSGVDILVK FFTSTPAAQE
LGB2_LUPLU--------GA LTESQAALVK SSWEEFNANI PKHTHRFFIL VLEIAPAAKD
FFESFGDLST PDAVMGNPKV KAHGKKVLGA FSDGLAHLDN LKGTFATLSE
FFDSFGDLSN PGAVMGNPKV KAHGKKVLHS FGEGVHHLDN LKGTFAALSE
FPTTKTYFPH FDLSHGSAQV KGHGKKVADA LTNAVAHVDD MPNALSALSD
FPTTKTYFPH FDLSHGSAQV KAHGKKVGDA LTLAVGHLDD LPGALSNLSD
KFDRFKHLKT EAEMKASEDL KKHGVTVLTA LGAILKKKGH HEAELKPLAQ
FFPKFKGLTT ADQLKKSADV RWHAERIINA VNDAVASMDD TEKMSMKLRD
LFSFLKGTSE VPQNNPELQA HAGKVFKLVY EAAIQLQVTG VVVTDATLKN
LHCDKLH--V DPENFRLLGN VLVCVLAHHF GKEFTPPVQA AYQKVVAGVA
LHCDKLH--V DPENFRLLGN VLVVVLARHF GKDFTPELQA SYQKVVAGVA
LHAHKLR--V DPVNFKLLSH CLLVTLAAHL PAEFTPAVHA SLDKFLASVS
LHAHKLR--V DPVNFKLLSH CLLSTLAVHL PNDFTPAVHA SLDKFLSSVS
SHATKHK--I PIKYLEFISE AIIHVLHSRH PGDFGADAQG AMNKALELFR
LSGKHAK--S FQVDPQYFKV LAAVIADTVA AGDAGFEKLM SMICILLRSA
LGSVHVSKGV ADAHFPVVKE AILKTIKEVV GAKWSEELNS AWTIAYDELA
NALAHKYH-- ----
NALAHKYH-- ----
TVLTSKYR-- ----
TVLTSKYR-- ----
KDIAAKYKEL GYQG
Y--------- ----
IVIKKEMNDA A---
7 167
HBB_HUMAN --------VH LTPEEKSAVT ALWGKVN--V DEVGGEALGR LLVVYPWTQR
HBB_HORSE --------VQ LSGEEKAAVL ALWDKVN--E EEVGGEALGR LLVVYPWTQR
HBA_HUMAN ---------V LSPADKTNVK AAWGKVGAHA GEYGAEALER MFLSFPTTKT
HBA_HORSE ---------V LSAADKTNVK AAWSKVGGHA GEYGAEALER MFLGFPTTKT
GLB5_PETMAPIVDTGSVAP LSAAEKTKIR SAWAPVYSTY ETSGVDILVK FFTSTPAAQE
MYG_PHYCA ---------V LSEGEWQLVL HVWAKVEADV AGHGQDILIR LFKSHPETLE
LGB2_LUPLU--------GA LTESQAALVK SSWEEFNANI PKHTHRFFIL VLEIAPAAKD
FFESFGDLST PDAVMGNPKV KAHGKKVLGA FSDGLAHLDN -----LKGTF
FFDSFGDLSN PGAVMGNPKV KAHGKKVLHS FGEGVHHLDN -----LKGTF
YFPHF-DLS- ----HGSAQV KGHGKKVADA LTNAVAHVDD -----MPNAL
YFPHF-DLS- ----HGSAQV KAHGKKVGDA LTLAVGHLDD -----LPGAL
FFPKFKGLTT ADQLKKSADV RWHAERIINA VNDAVASMDD T--EKMSMKL
KFDRFKHLKT EAEMKASEDL KKHGVTVLTA LGAILKKKGH -----HEAEL
LFSFLKGTSE VP--QNNPEL QAHAGKVFKL VYEAAIQLQV TGVVVTDATL
ATLSELHCDK LHVDPENFRL LGNVLVCVLA HHFGKEFTPP VQAAYQKVVA
AALSELHCDK LHVDPENFRL LGNVLVVVLA RHFGKDFTPE LQASYQKVVA
SALSDLHAHK LRVDPVNFKL LSHCLLVTLA AHLPAEFTPA VHASLDKFLA
SNLSDLHAHK LRVDPVNFKL LSHCLLSTLA VHLPNDFTPA VHASLDKFLS
RDLSGKHAKS FQVDPQYFKV LAAVIADTVA AG-------- -DAGFEKLMS
KPLAQSHATK HKIPIKYLEF ISEAIIHVLH SRHPGDFGAD AQGAMNKALE
KNLGSVHVSK G-VADAHFPV VKEAILKTIK EVVGAKWSEE LNSAWTIAYD
GVANALAHKY H------
GVANALAHKY H------
SVSTVLTSKY R------
SVSTVLTSKY R------
MICILLRSAY -------
LFRKDIAAKY KELGYQG
ELAIVIKKEM NDAA---
|
7 164
HBB_HUMAN --------VH LTPEEKSAVT ALWGKVN-VD EVGGEALGR- LLVVYPWTQR
HBB_HORSE --------VQ LSGEEKAAVL ALWDKVN-EE EVGGEALGR- LLVVYPWTQR
HBA_HUMAN ---------- ----VLSPAD KTNVKAA-WG KVGAHAGEYG AEALERMFLS
HBA_HORSE ---------- ----VLSAAD KTNVKAA-WS KVGGHAGEYG AEALERMFLG
MYG_PHYCA -------VLS EGEWQLVLHV WAKVEAD-VA GHGQDILIR- LFKSHPETLE
GLB5_PETMAPIVDTGSVAP LSAAEKTKIR SAWAPVYSTY ETSGVDILVK FFTSTPAAQE
LGB2_LUPLU--------GA LTESQAALVK SSWEEFNANI PKHTHRFFIL VLEIAPAAKD
FFESFGDLST PDAVMGNPKV KAHGKKVLGA FSDGLAHLDN LKGTFATLSE
FFDSFGDLSN PGAVMGNPKV KAHGKKVLHS FGEGVHHLDN LKGTFAALSE
FPTTKTYFPH FDLSHGSAQV KGHGKKVADA LTNAVAHVDD MPNALSALSD
FPTTKTYFPH FDLSHGSAQV KAHGKKVGDA LTLAVGHLDD LPGALSNLSD
KFDRFKHLKT EAEMKASEDL KKHGVTVLTA LGAILKKKGH HEAELKPLAQ
FFPKFKGLTT ADQLKKSADV RWHAERIINA VNDAVASMDD TEKMSMKLRD
LFSFLKGTSE VPQNNPELQA HAGKVFKLVY EAAIQLQVTG VVVTDATLKN
LHCDKLH--V DPENFRLLGN VLVCVLAHHF GKEFTPPVQA AYQKVVAGVA
LHCDKLH--V DPENFRLLGN VLVVVLARHF GKDFTPELQA SYQKVVAGVA
LHAHKLR--V DPVNFKLLSH CLLVTLAAHL PAEFTPAVHA SLDKFLASVS
LHAHKLR--V DPVNFKLLSH CLLSTLAVHL PNDFTPAVHA SLDKFLSSVS
SHATKHK--I PIKYLEFISE AIIHVLHSRH PGDFGADAQG AMNKALELFR
LSGKHAK--S FQVDPQYFKV LAAVIADTVA AGDAGFEKLM SMICILLRSA
LGSVHVSKGV ADAHFPVVKE AILKTIKEVV GAKWSEELNS AWTIAYDELA
NALAHKYH-- ----
NALAHKYH-- ----
TVLTSKYR-- ----
TVLTSKYR-- ----
KDIAAKYKEL GYQG
Y--------- ----
IVIKKEMNDA A---
7 167
HBB_HUMAN --------VH LTPEEKSAVT ALWGKVN--V DEVGGEALGR LLVVYPWTQR
HBB_HORSE --------VQ LSGEEKAAVL ALWDKVN--E EEVGGEALGR LLVVYPWTQR
HBA_HUMAN ---------V LSPADKTNVK AAWGKVGAHA GEYGAEALER MFLSFPTTKT
HBA_HORSE ---------V LSAADKTNVK AAWSKVGGHA GEYGAEALER MFLGFPTTKT
GLB5_PETMAPIVDTGSVAP LSAAEKTKIR SAWAPVYSTY ETSGVDILVK FFTSTPAAQE
MYG_PHYCA ---------V LSEGEWQLVL HVWAKVEADV AGHGQDILIR LFKSHPETLE
LGB2_LUPLU--------GA LTESQAALVK SSWEEFNANI PKHTHRFFIL VLEIAPAAKD
FFESFGDLST PDAVMGNPKV KAHGKKVLGA FSDGLAHLDN -----LKGTF
FFDSFGDLSN PGAVMGNPKV KAHGKKVLHS FGEGVHHLDN -----LKGTF
YFPHF-DLS- ----HGSAQV KGHGKKVADA LTNAVAHVDD -----MPNAL
YFPHF-DLS- ----HGSAQV KAHGKKVGDA LTLAVGHLDD -----LPGAL
FFPKFKGLTT ADQLKKSADV RWHAERIINA VNDAVASMDD T--EKMSMKL
KFDRFKHLKT EAEMKASEDL KKHGVTVLTA LGAILKKKGH -----HEAEL
LFSFLKGTSE VP--QNNPEL QAHAGKVFKL VYEAAIQLQV TGVVVTDATL
ATLSELHCDK LHVDPENFRL LGNVLVCVLA HHFGKEFTPP VQAAYQKVVA
AALSELHCDK LHVDPENFRL LGNVLVVVLA RHFGKDFTPE LQASYQKVVA
SALSDLHAHK LRVDPVNFKL LSHCLLVTLA AHLPAEFTPA VHASLDKFLA
SNLSDLHAHK LRVDPVNFKL LSHCLLSTLA VHLPNDFTPA VHASLDKFLS
RDLSGKHAKS FQVDPQYFKV LAAVIADTVA AG-------- -DAGFEKLMS
KPLAQSHATK HKIPIKYLEF ISEAIIHVLH SRHPGDFGAD AQGAMNKALE
KNLGSVHVSK G-VADAHFPV VKEAILKTIK EVVGAKWSEE LNSAWTIAYD
GVANALAHKY H------
GVANALAHKY H------
SVSTVLTSKY R------
SVSTVLTSKY R------
MICILLRSAY -------
LFRKDIAAKY KELGYQG
ELAIVIKKEM NDAA---
|
| 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 |
| nthseqset | Reads and writes (returns) one set of sequences from many |
| 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 |
| 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 |
| 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 |