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eomegaps |
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Clustal-Omega (clustalo) is a general purpose multiple sequence alignment (MSA) program for proteins. It produces high quality MSAs and is capable of handling data-sets of hundreds of thousands of sequences in reasonable time.
In its current form Clustal-Omega can only align protein sequences but not DNA/RNA sequences. It is envisioned that DNA/RNA will become available in a future version.
% eomegaps op1.ali tsw:opsd_human Single sequence with profile (ClustalO wrapper) (aligned) output sequence set [op1.aln]: |
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Go to the output files for this example
Single sequence with profile (ClustalO wrapper) Version: EMBOSS:6.6.0.0 Standard (Mandatory) qualifiers: [-profile] infile Pre-aligned multiple sequence file (aligned columns will be kept fixed) [-sequence] sequence File containing single sequence to align [-outseq] seqoutset [ |
Qualifier | Type | Description | Allowed values | Default | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Standard (Mandatory) qualifiers | ||||||||||||||||||
[-profile] (Parameter 1) |
infile | Pre-aligned multiple sequence file (aligned columns will be kept fixed) | Input file | Required | ||||||||||||||
[-sequence] (Parameter 2) |
sequence | File containing single sequence to align | Readable sequence | Required | ||||||||||||||
[-outseq] (Parameter 3) |
seqoutset | Sequence set filename and optional format (output USA) | Writeable sequences | <*>.format | ||||||||||||||
Additional (Optional) qualifiers | ||||||||||||||||||
(none) | ||||||||||||||||||
Advanced (Unprompted) qualifiers | ||||||||||||||||||
-indistfile | infile | Pairwise distance matrix input file (skips distance computation) | Input file | Required | ||||||||||||||
-inguidefile | infile | Guide tree input file (skips distance computation and guide tree clustering step) | Input file | Required | ||||||||||||||
-dealign | toggle | Dealign input sequences | Toggle value Yes/No | No | ||||||||||||||
-cluster | list | Method |
|
mbed | ||||||||||||||
-maxiterations | integer | Number of (combined guide tree/HMM) iterations | Integer from 0 to 2000000000 | 0 | ||||||||||||||
-maxgiterations | integer | Maximum guide tree iterations | Integer from 0 to 2000000000 | 2000000000 | ||||||||||||||
-maxhiterations | integer | Maximum number of HMM iterations | Integer from 0 to 2000000000 | 2000000000 | ||||||||||||||
-maxseqs | integer | Maximum number of sequences | Integer from 2 to 2000000000 | 2000000000 | ||||||||||||||
-maxlenseq | integer | Maximum length of sequence | Integer from 1 to 2000000000 | 2000000000 | ||||||||||||||
-self | toggle | Set options automatically (might overwrite some options | Toggle value Yes/No | No | ||||||||||||||
-outformat | list | Format |
|
fasta | ||||||||||||||
-outdistfile | outfile | Pairwise distance matrix output file, only available in cluster mode 'full' | Output file | <*>.eomegaps | ||||||||||||||
-outguidefile | outfile | Guide tree output file | Output file | <*>.eomegaps | ||||||||||||||
-log | toggle | Log progress to standard output if not used for output | Toggle value Yes/No | No | ||||||||||||||
Associated qualifiers | ||||||||||||||||||
"-sequence" associated sequence qualifiers | ||||||||||||||||||
-sbegin2 -sbegin_sequence |
integer | Start of the sequence to be used | Any integer value | 0 | ||||||||||||||
-send2 -send_sequence |
integer | End of the sequence to be used | Any integer value | 0 | ||||||||||||||
-sreverse2 -sreverse_sequence |
boolean | Reverse (if DNA) | Boolean value Yes/No | N | ||||||||||||||
-sask2 -sask_sequence |
boolean | Ask for begin/end/reverse | Boolean value Yes/No | N | ||||||||||||||
-snucleotide2 -snucleotide_sequence |
boolean | Sequence is nucleotide | Boolean value Yes/No | N | ||||||||||||||
-sprotein2 -sprotein_sequence |
boolean | Sequence is protein | Boolean value Yes/No | N | ||||||||||||||
-slower2 -slower_sequence |
boolean | Make lower case | Boolean value Yes/No | N | ||||||||||||||
-supper2 -supper_sequence |
boolean | Make upper case | Boolean value Yes/No | N | ||||||||||||||
-scircular2 -scircular_sequence |
boolean | Sequence is circular | Boolean value Yes/No | N | ||||||||||||||
-squick2 -squick_sequence |
boolean | Read id and sequence only | Boolean value Yes/No | N | ||||||||||||||
-sformat2 -sformat_sequence |
string | Input sequence format | Any string | |||||||||||||||
-iquery2 -iquery_sequence |
string | Input query fields or ID list | Any string | |||||||||||||||
-ioffset2 -ioffset_sequence |
integer | Input start position offset | Any integer value | 0 | ||||||||||||||
-sdbname2 -sdbname_sequence |
string | Database name | Any string | |||||||||||||||
-sid2 -sid_sequence |
string | Entryname | Any string | |||||||||||||||
-ufo2 -ufo_sequence |
string | UFO features | Any string | |||||||||||||||
-fformat2 -fformat_sequence |
string | Features format | Any string | |||||||||||||||
-fopenfile2 -fopenfile_sequence |
string | Features file name | Any string | |||||||||||||||
"-outseq" associated seqoutset qualifiers | ||||||||||||||||||
-osformat3 -osformat_outseq |
string | Output seq format | Any string | |||||||||||||||
-osextension3 -osextension_outseq |
string | File name extension | Any string | |||||||||||||||
-osname3 -osname_outseq |
string | Base file name | Any string | |||||||||||||||
-osdirectory3 -osdirectory_outseq |
string | Output directory | Any string | |||||||||||||||
-osdbname3 -osdbname_outseq |
string | Database name to add | Any string | |||||||||||||||
-ossingle3 -ossingle_outseq |
boolean | Separate file for each entry | Boolean value Yes/No | N | ||||||||||||||
-oufo3 -oufo_outseq |
string | UFO features | Any string | |||||||||||||||
-offormat3 -offormat_outseq |
string | Features format | Any string | |||||||||||||||
-ofname3 -ofname_outseq |
string | Features file name | Any string | |||||||||||||||
-ofdirectory3 -ofdirectory_outseq |
string | Output directory | Any string | |||||||||||||||
"-outdistfile" associated outfile qualifiers | ||||||||||||||||||
-odirectory | string | Output directory | Any string | |||||||||||||||
"-outguidefile" associated outfile qualifiers | ||||||||||||||||||
-odirectory | 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 |
>OPSD_ABYKO O42294 Rhodopsin (Fragment) -----------------------------------------YLVNPAAYAALGAYMFLLI LIGFP---INFLTLYVTLEHKKLRTPLNYILLNLAVANLFMVLGGFTTTMYTSMHGYFVL GRLGCNLEAFFATLGGEIALWSLVVLAIERWIVVCKPISNFRFTEDHAIMGLAFTWVMAL ACAVPPLVGWSRYIPEGMQCSCGVDYYTRAEGFNNESFVIYMFIVHFLIPLSVIFFCYGR LLCAVKEAPAAQQE-------------SETTQRAEKEVSRMVVIMVIGFLVCWLPYASVA WWIFCNQGSDFGPIFMTLPSFFAKSAAIYNPMIYICMNKQFRHCMI-------------- ------------------------- >OPSD_AMBTI Q90245 Rhodopsin MNGTEGPNFYV-------PFSNKSGVVRSPFEYP-----QYYLAEPWQYSVLAAYMFLLI LLGFP---VNFLTLYVTIQHKKLRTPLNYILLNLAFANHFMVFGGFPVTMYSSMHGYFVF GQTGCYIEGFFATMGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVMMTWIMAL ACAAPPLFGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFLVHFTIPLMIIFFCYGR LVCTVKEAAAQQQE-------------SATTQKAEKEVTRMVIIMVVAFLICWVPYASVA FYIFSNQGTDFGPIFMTVPAFFAKSSAIYNPVIYIVLNKQFRNCMIT---TICCGKNPFG DDETTSAATSKTEASSVSSSQVSPA >OPSD_ANOCA P41591 Rhodopsin MNGTEGQNFYV-------PMSNKTGVVRNPFEYP-----QYYLADPWQFSALAAYMFLLI LLGFP---INFLTLFVTIQHKKLRTPLNYILLNLAVANLFMVLMGFTTTMYTSMNGYFIF GTVGCNIEGFFATLGGEMGLWSLVVLAVERYVVICKPMSNFRFGETHALIGVSCTWIMAL ACAGPPLLGWSRYIPEGMQCSCGVDYYTPTPEVHNESFVIYMFLVHFVTPLTIIFFCYGR LVCTVKAAAAQQQE-------------SATTQKAEREVTRMVVIMVISFLVCWVPYASVA FYIFTHQGSDFGPVFMTIPAFFAKSSAIYNPVIYILMNKQFRNCMIM---TLCCGKNPLG DEETSAG--TKTETSTVSTSQVSPA >OPSD_APIME Q17053 Rhodopsin, long-wavelength (Opsin, green-sensitive) MIAVSGPSYEAFSYGGQARFNNQTVVDKVPPDMLHLIDANWYQYPPLNPMWHGILGFVIG MLGFVSAMGNGMVVYIFLSTKSLRTPSNLFVINLAISNFLMMFCMSPPMVINCYYETWVL GPLFCQIYAMLGSLFGCGSIWTMTMIAFDRYNVIVKGLSGKPLSINGALIRIIAIWLFSL GWTIAPMFGWNRYVPEGNMTACGTDYFNRGL--LSASYLVCYGIWVYFVPLFLIIYSYWF IIQAVAAHEKNMREQAKKMNVASLRSSENQNTSAECKLAKVALMTISLWFMAWTPYLVIN FSGIF-NLVKISPLFTIWGSLFAKANAVYNPIVYGISHPKYRAALFAKFPSLACAAEPSS DAVSTTSGTTTVTD-----NEKSNA >OPSD_ASTFA P41590 Rhodopsin MNGTEGPYFYV-------PMSNATGVVRSPYEYP-----QYYLAPPWAYACLAAYMFFLI LVGFP---VNFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSLNGYFVF GRLGCNLEGFFATFGGINSLWCLVVLSIERWVVVCKPMSNFRFGENHAIMGVAFTWFMAL ACTVPPLVGWSRYIPEGMQCSCGIDYYTRAEGFNNESFVIYMFVVHFLTPLFVITFCYGR LVCTVKEAAAQQQE-------------SETTQRAEREVTRMVILMFIAYLVCWLPYASVS WWIFTNQGSEFGPIFMTVPAFFAKSSSIYNPVIYICLNKQFRHCMIT---TLCCGKNPFE EEEGASTTASKTEASSVSSVSPA-- >OPSD_ATHBO Q9YGZ1 Rhodopsin MNGTEGPYFYI-------PMLNTTGVVRSPYEYP-----QYYLVNPAAYAVLGAYMFFLI LVGFP---INFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTIYTSMHGYFVL GRLGCNVEGFSATLGGEIALWSLVVLAIERWVVVCKPISNFRFGENHAIMGVAFTWFMAA ACAVPPLFGWSRYIPEGMQCSCGIDYYTRAEGFNNESFVIYMFTCHFCIPLMVVFFCYGR LVCAVKEAAAAQQE-------------SETTQRAEREVTRMVIIMVVSFLVSWVPYASVA WYIFTHQGSEFGPLFMTIPAFFAKSSSIYNPMIYICMNKQFRHCMIT---TLCCGKNPFE EEEGASSTASKTEASSVSSSSVSPA >OPSD_BATMU O42300 Rhodopsin (Fragment) -----------------------------------------YLVSPAAYAALGAYMFLLI LIGFP---VNFLTLYVTLEHKKLRTPLNYILLNLAVADLFMVLGGFTTTMYTSMHGYFVL GRLGCNLEGFFATLGGEIALWSLVVLAIERWIVVCKPISNFRFTEDNAIMGLAFSWVMAL TCAVPPLVGWSRYIPEGMQCSCGVDYYTRAEGFNNESFVIYMFIVHFPIPLSVIFFCYGR LLCAVKEAAAAQQE-------------SETTQRAEKEVSRMVVILVIGFLVCWLPYASVA WWIFCNQGSDFGPIFMTLPSFFAKRPAIYNPMIYICMNKQFRHCMI-------------- ------------------------- >OPSD_BATNI O42301 Rhodopsin (Fragment) -----------------------------------------YLVSPAAYAALGAYMFLLI LIGFP---VNFLTLYVTLEHKKLRTPLNYILLNLAVADLFMVLGGFTTTMYTSMHGYFVL GRLGCNLEGFFATLGGEIALWSLVVLAIERWIVVCKPISKFRFTEDNAIMGLAFSWVMAL ACAVPPLVGWLRYIPEGMQCTCGVDYYTRAEGFDNESFVIYMFIVHFLIPLSVIFFCYGR LLCAVKEAAAAQQE-------------SETTQRAEKEVSRMVVIMVIGFLVCWLPYASVA WWIFCNQGSDFGPIFMTLPSFFAKRPAIYNPMIYICMNKQFRHCMI-------------- ------------------------- >OPSD_BOVIN P02699 Rhodopsin MNGTEGPNFYV-------PFSNKTGVVRSPFEAP-----QYYLAEPWQFSMLAAYMFLLI MLGFP---INFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVF GPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMAL ACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQ LVFTVKEAAAQQQE-------------SATTQKAEKEVTRMVIIMVIAFLICWLPYAGVA FYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVT---TLCCGKNPLG DDEASTTVS-KTET-----SQVAPA >OPSD_BUFBU P56514 Rhodopsin MNGTEGPNFYI-------PMSNKTGVVRSPFEYP-----QYYLAEPWQYSILCAYMFLLI LLGFP---INFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFIL GATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMAL SCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGR LVCTVKEAAAQQQE-------------SATTQKAEKEVTRMVIIMVVFFLICWVPYASVA FFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMIT---TLCCGKNPFG EDDASSAATSKTEASSVSSSQVSPA >OPSD_BUFMA P56515 Rhodopsin MNGTEGPNFYI-------PMSNKTGVVRSPFEYP-----QYYLAEPWQYSVLCAYMFLLI LLGFP---INFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFVF GQTGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAIMGVAFTWIMAL ACAAPPLFGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFLIPLIIIFFCYGR LVCTVKEAAAQQQE-------------SATTQKAEKEVTRMVIIMVVFFLICWVPYASVA FFIFTHQGSEFGPVFMTIPAFFAKSSSIYNPVIYIMLNKQFRNCMIT---TLCCGKNPFG DEDASSAATSKTEASSVSSSQVSPA >OPSD_CALPD Q6W3E1 Rhodopsin MNGTEGPNFYV-------PFSNKTGVVRSPFEEP-----QYYLAEPWQFSCLAAYMFMLI VLGFP---INFLTLYVTIQHKKLRTPLNYILLNLAIADLFMVFGGFTTTLYTSLHGYFVF GPTGCDLEGFFATLGGEIALWSLVVLAIERYIVVCKPMSNFRFGENHAIMGVAFTWVMAL ACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMVVIFFCYGQ LVFTVKEAAAQQQE-------------SATTQKAEKEVTRMVIIMVIAFLICWLPYAGVA FYIFTHQGSNFGPILMTLPAFFAKTSAVYNPVIYIMLNKQFRTCMLT---TLCCGKIPLG DDEASATAS-KTET-----SQVAPA |
ID OPSD_HUMAN Reviewed; 348 AA. AC P08100; Q16414; Q2M249; DT 01-AUG-1988, integrated into UniProtKB/Swiss-Prot. DT 01-AUG-1988, sequence version 1. DT 13-JUN-2012, entry version 145. DE RecName: Full=Rhodopsin; DE AltName: Full=Opsin-2; GN Name=RHO; Synonyms=OPN2; OS Homo sapiens (Human). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; OC Catarrhini; Hominidae; Homo. OX NCBI_TaxID=9606; RN [1] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA]. RX MEDLINE=84272729; PubMed=6589631; DOI=10.1073/pnas.81.15.4851; RA Nathans J., Hogness D.S.; RT "Isolation and nucleotide sequence of the gene encoding human RT rhodopsin."; RL Proc. Natl. Acad. Sci. U.S.A. 81:4851-4855(1984). RN [2] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA]. RA Suwa M., Sato T., Okouchi I., Arita M., Futami K., Matsumoto S., RA Tsutsumi S., Aburatani H., Asai K., Akiyama Y.; RT "Genome-wide discovery and analysis of human seven transmembrane helix RT receptor genes."; RL Submitted (JUL-2001) to the EMBL/GenBank/DDBJ databases. RN [3] RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. RC TISSUE=Retina; RX PubMed=17974005; DOI=10.1186/1471-2164-8-399; RA Bechtel S., Rosenfelder H., Duda A., Schmidt C.P., Ernst U., RA Wellenreuther R., Mehrle A., Schuster C., Bahr A., Bloecker H., RA Heubner D., Hoerlein A., Michel G., Wedler H., Koehrer K., RA Ottenwaelder B., Poustka A., Wiemann S., Schupp I.; RT "The full-ORF clone resource of the German cDNA consortium."; RL BMC Genomics 8:399-399(2007). RN [4] RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. RX PubMed=15489334; DOI=10.1101/gr.2596504; RG The MGC Project Team; RT "The status, quality, and expansion of the NIH full-length cDNA RT project: the Mammalian Gene Collection (MGC)."; RL Genome Res. 14:2121-2127(2004). RN [5] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-120. RX PubMed=8566799; DOI=10.1016/0378-1119(95)00688-5; RA Bennett J., Beller B., Sun D., Kariko K.; RT "Sequence analysis of the 5.34-kb 5' flanking region of the human RT rhodopsin-encoding gene."; [Part of this file has been deleted for brevity] FT /FTId=VAR_004816. FT VARIANT 209 209 V -> M (effect not known). FT /FTId=VAR_004817. FT VARIANT 211 211 H -> P (in RP4; dbSNP:rs28933993). FT /FTId=VAR_004818. FT VARIANT 211 211 H -> R (in RP4). FT /FTId=VAR_004819. FT VARIANT 216 216 M -> K (in RP4). FT /FTId=VAR_004820. FT VARIANT 220 220 F -> C (in RP4). FT /FTId=VAR_004821. FT VARIANT 222 222 C -> R (in RP4). FT /FTId=VAR_004822. FT VARIANT 255 255 Missing (in RP4). FT /FTId=VAR_004823. FT VARIANT 264 264 Missing (in RP4). FT /FTId=VAR_004824. FT VARIANT 267 267 P -> L (in RP4). FT /FTId=VAR_004825. FT VARIANT 267 267 P -> R (in RP4). FT /FTId=VAR_004826. FT VARIANT 292 292 A -> E (in CSNBAD1). FT /FTId=VAR_004827. FT VARIANT 296 296 K -> E (in RP4; dbSNP:rs29001653). FT /FTId=VAR_004828. FT VARIANT 297 297 S -> R (in RP4). FT /FTId=VAR_004829. FT VARIANT 342 342 T -> M (in RP4). FT /FTId=VAR_004830. FT VARIANT 345 345 V -> L (in RP4). FT /FTId=VAR_004831. FT VARIANT 345 345 V -> M (in RP4). FT /FTId=VAR_004832. FT VARIANT 347 347 P -> A (in RP4). FT /FTId=VAR_004833. FT VARIANT 347 347 P -> L (in RP4; common variant). FT /FTId=VAR_004834. FT VARIANT 347 347 P -> Q (in RP4). FT /FTId=VAR_004835. FT VARIANT 347 347 P -> R (in RP4; dbSNP:rs29001566). FT /FTId=VAR_004836. FT VARIANT 347 347 P -> S (in RP4; dbSNP:rs29001637). FT /FTId=VAR_004837. SQ SEQUENCE 348 AA; 38893 MW; 6F4F6FCBA34265B2 CRC64; MNGTEGPNFY VPFSNATGVV RSPFEYPQYY LAEPWQFSML AAYMFLLIVL GFPINFLTLY VTVQHKKLRT PLNYILLNLA VADLFMVLGG FTSTLYTSLH GYFVFGPTGC NLEGFFATLG GEIALWSLVV LAIERYVVVC KPMSNFRFGE NHAIMGVAFT WVMALACAAP PLAGWSRYIP EGLQCSCGID YYTLKPEVNN ESFVIYMFVV HFTIPMIIIF FCYGQLVFTV KEAAAQQQES ATTQKAEKEV TRMVIIMVIA FLICWVPYAS VAFYIFTHQG SNFGPIFMTI PAFFAKSAAI YNPVIYIMMN KQFRNCMLTT ICCGKNPLGD DEASATVSKT ETSQVAPA // |
>OPSD_HUMAN P08100 Rhodopsin (Opsin-2) MNGTEGPNFYV-------PFSNATGVVRSPFEYP-----QYYLAEPWQFSMLAAYMFLLI VLGFP---INFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVF GPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMAL ACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQ LVFTVKEAAAQQQE-------------SATTQKAEKEVTRMVIIMVIAFLICWVPYASVA FYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLT---TICCGKNPLG DDEASATVS-KTET-----SQVAPA >OPSD_ABYKO O42294 Rhodopsin (Fragment) -----------------------------------------YLVNPAAYAALGAYMFLLI LIGFP---INFLTLYVTLEHKKLRTPLNYILLNLAVANLFMVLGGFTTTMYTSMHGYFVL GRLGCNLEAFFATLGGEIALWSLVVLAIERWIVVCKPISNFRFTEDHAIMGLAFTWVMAL ACAVPPLVGWSRYIPEGMQCSCGVDYYTRAEGFNNESFVIYMFIVHFLIPLSVIFFCYGR LLCAVKEAPAAQQE-------------SETTQRAEKEVSRMVVIMVIGFLVCWLPYASVA WWIFCNQGSDFGPIFMTLPSFFAKSAAIYNPMIYICMNKQFRHCMI-------------- ------------------------- >OPSD_AMBTI Q90245 Rhodopsin MNGTEGPNFYV-------PFSNKSGVVRSPFEYP-----QYYLAEPWQYSVLAAYMFLLI LLGFP---VNFLTLYVTIQHKKLRTPLNYILLNLAFANHFMVFGGFPVTMYSSMHGYFVF GQTGCYIEGFFATMGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVMMTWIMAL ACAAPPLFGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFLVHFTIPLMIIFFCYGR LVCTVKEAAAQQQE-------------SATTQKAEKEVTRMVIIMVVAFLICWVPYASVA FYIFSNQGTDFGPIFMTVPAFFAKSSAIYNPVIYIVLNKQFRNCMIT---TICCGKNPFG DDETTSAATSKTEASSVSSSQVSPA >OPSD_ANOCA P41591 Rhodopsin MNGTEGQNFYV-------PMSNKTGVVRNPFEYP-----QYYLADPWQFSALAAYMFLLI LLGFP---INFLTLFVTIQHKKLRTPLNYILLNLAVANLFMVLMGFTTTMYTSMNGYFIF GTVGCNIEGFFATLGGEMGLWSLVVLAVERYVVICKPMSNFRFGETHALIGVSCTWIMAL ACAGPPLLGWSRYIPEGMQCSCGVDYYTPTPEVHNESFVIYMFLVHFVTPLTIIFFCYGR LVCTVKAAAAQQQE-------------SATTQKAEREVTRMVVIMVISFLVCWVPYASVA FYIFTHQGSDFGPVFMTIPAFFAKSSAIYNPVIYILMNKQFRNCMIM---TLCCGKNPLG DEETSAG--TKTETSTVSTSQVSPA >OPSD_APIME Q17053 Rhodopsin, long-wavelength (Opsin, green-sensitive) MIAVSGPSYEAFSYGGQARFNNQTVVDKVPPDMLHLIDANWYQYPPLNPMWHGILGFVIG MLGFVSAMGNGMVVYIFLSTKSLRTPSNLFVINLAISNFLMMFCMSPPMVINCYYETWVL GPLFCQIYAMLGSLFGCGSIWTMTMIAFDRYNVIVKGLSGKPLSINGALIRIIAIWLFSL GWTIAPMFGWNRYVPEGNMTACGTDYFNRGL--LSASYLVCYGIWVYFVPLFLIIYSYWF IIQAVAAHEKNMREQAKKMNVASLRSSENQNTSAECKLAKVALMTISLWFMAWTPYLVIN FSGIF-NLVKISPLFTIWGSLFAKANAVYNPIVYGISHPKYRAALFAKFPSLACAAEPSS DAVSTTSGTTTVTD-----NEKSNA >OPSD_ASTFA P41590 Rhodopsin MNGTEGPYFYV-------PMSNATGVVRSPYEYP-----QYYLAPPWAYACLAAYMFFLI LVGFP---VNFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSLNGYFVF GRLGCNLEGFFATFGGINSLWCLVVLSIERWVVVCKPMSNFRFGENHAIMGVAFTWFMAL ACTVPPLVGWSRYIPEGMQCSCGIDYYTRAEGFNNESFVIYMFVVHFLTPLFVITFCYGR LVCTVKEAAAQQQE-------------SETTQRAEREVTRMVILMFIAYLVCWLPYASVS WWIFTNQGSEFGPIFMTVPAFFAKSSSIYNPVIYICLNKQFRHCMIT---TLCCGKNPFE EEEGASTTASKTEASSVSSVSPA-- >OPSD_ATHBO Q9YGZ1 Rhodopsin MNGTEGPYFYI-------PMLNTTGVVRSPYEYP-----QYYLVNPAAYAVLGAYMFFLI [Part of this file has been deleted for brevity] LVCAVKEAAAAQQE-------------SETTQRAEREVTRMVIIMVVSFLVSWVPYASVA WYIFTHQGSEFGPLFMTIPAFFAKSSSIYNPMIYICMNKQFRHCMIT---TLCCGKNPFE EEEGASSTASKTEASSVSSSSVSPA >OPSD_BATMU O42300 Rhodopsin (Fragment) -----------------------------------------YLVSPAAYAALGAYMFLLI LIGFP---VNFLTLYVTLEHKKLRTPLNYILLNLAVADLFMVLGGFTTTMYTSMHGYFVL GRLGCNLEGFFATLGGEIALWSLVVLAIERWIVVCKPISNFRFTEDNAIMGLAFSWVMAL TCAVPPLVGWSRYIPEGMQCSCGVDYYTRAEGFNNESFVIYMFIVHFPIPLSVIFFCYGR LLCAVKEAAAAQQE-------------SETTQRAEKEVSRMVVILVIGFLVCWLPYASVA WWIFCNQGSDFGPIFMTLPSFFAKRPAIYNPMIYICMNKQFRHCMI-------------- ------------------------- >OPSD_BATNI O42301 Rhodopsin (Fragment) -----------------------------------------YLVSPAAYAALGAYMFLLI LIGFP---VNFLTLYVTLEHKKLRTPLNYILLNLAVADLFMVLGGFTTTMYTSMHGYFVL GRLGCNLEGFFATLGGEIALWSLVVLAIERWIVVCKPISKFRFTEDNAIMGLAFSWVMAL ACAVPPLVGWLRYIPEGMQCTCGVDYYTRAEGFDNESFVIYMFIVHFLIPLSVIFFCYGR LLCAVKEAAAAQQE-------------SETTQRAEKEVSRMVVIMVIGFLVCWLPYASVA WWIFCNQGSDFGPIFMTLPSFFAKRPAIYNPMIYICMNKQFRHCMI-------------- ------------------------- >OPSD_BOVIN P02699 Rhodopsin MNGTEGPNFYV-------PFSNKTGVVRSPFEAP-----QYYLAEPWQFSMLAAYMFLLI MLGFP---INFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVF GPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMAL ACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQ LVFTVKEAAAQQQE-------------SATTQKAEKEVTRMVIIMVIAFLICWLPYAGVA FYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVT---TLCCGKNPLG DDEASTTVS-KTET-----SQVAPA >OPSD_BUFBU P56514 Rhodopsin MNGTEGPNFYI-------PMSNKTGVVRSPFEYP-----QYYLAEPWQYSILCAYMFLLI LLGFP---INFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFIL GATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMAL SCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGR LVCTVKEAAAQQQE-------------SATTQKAEKEVTRMVIIMVVFFLICWVPYASVA FFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMIT---TLCCGKNPFG EDDASSAATSKTEASSVSSSQVSPA >OPSD_BUFMA P56515 Rhodopsin MNGTEGPNFYI-------PMSNKTGVVRSPFEYP-----QYYLAEPWQYSVLCAYMFLLI LLGFP---INFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFVF GQTGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAIMGVAFTWIMAL ACAAPPLFGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFLIPLIIIFFCYGR LVCTVKEAAAQQQE-------------SATTQKAEKEVTRMVIIMVVFFLICWVPYASVA FFIFTHQGSEFGPVFMTIPAFFAKSSSIYNPVIYIMLNKQFRNCMIT---TLCCGKNPFG DEDASSAATSKTEASSVSSSQVSPA >OPSD_CALPD Q6W3E1 Rhodopsin MNGTEGPNFYV-------PFSNKTGVVRSPFEEP-----QYYLAEPWQFSCLAAYMFMLI VLGFP---INFLTLYVTIQHKKLRTPLNYILLNLAIADLFMVFGGFTTTLYTSLHGYFVF GPTGCDLEGFFATLGGEIALWSLVVLAIERYIVVCKPMSNFRFGENHAIMGVAFTWVMAL ACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMVVIFFCYGQ LVFTVKEAAAQQQE-------------SATTQKAEKEVTRMVIIMVIAFLICWLPYAGVA FYIFTHQGSNFGPILMTLPAFFAKTSAVYNPVIYIMLNKQFRTCMLT---TLCCGKIPLG DDEASATAS-KTET-----SQVAPA |
[2] Blackshields G, Sievers F, Shi W, Wilm A, Higgins DG. Sequence embedding for fast construction of guide trees for multiple sequence alignment. Algorithms Mol Biol. 2010 May 14;5:21.
[3] http://www.genetics.wustl.edu/eddy/software/#squid
[4] Wilbur and Lipman, 1983; PMID 6572363
[5] Thompson JD, Higgins DG, Gibson TJ. (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.
[6] Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG. (2007). Clustal W and Clustal X version 2.0. Bioinformatics, 23, 2947-2948.
[7] Kimura M (1980). "A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences". Journal of Molecular Evolution 16: 111–120.
[8] Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput.Nucleic Acids Res. 32(5):1792-1797.
Program name | Description |
---|---|
edialign | Local multiple alignment of sequences |
emma | Multiple sequence alignment (ClustalW wrapper) |
eomega | Multiple sequence alignment (ClustalO wrapper) |
eomegapp | Profile with profile (ClustalO wrapper) |
eomegash | Sequence with HMM (ClustalO wrapper) |
eomegasp | Sequence with profile (ClustalO wrapper) |
infoalign | Display basic information about a multiple sequence alignment |
mse | Multiple sequence editor |
plotcon | Plot conservation of a sequence alignment |
prettyplot | Draw a sequence alignment with pretty formatting |
showalign | Display a multiple sequence alignment in pretty format |
tranalign | Generate an alignment of nucleic coding regions from aligned proteins |
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.