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seqretsetall |
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% seqretsetall -osf phylip Read and write (return) 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
Read and write (return) many sets of sequences
Version: EMBOSS:6.6.0.0
Standard (Mandatory) qualifiers:
[-sequence] seqsetall Sequence set(s) filename and optional
format, or reference (input USA)
[-outseq] seqoutall [
|
| Qualifier | Type | Description | Allowed values | Default |
|---|---|---|---|---|
| Standard (Mandatory) qualifiers | ||||
| [-sequence] (Parameter 1) |
seqsetall | Sequence set(s) filename and optional format, or reference (input USA) | Readable sets of sequences | 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 |
| Associated qualifiers | ||||
| "-sequence" associated seqsetall 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 |
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---
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| 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 |
| seqret | Read and write (return) 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 |
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.