eomegapp

 

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Function

Profile with profile (ClustalO wrapper)

Description

eomegapp is a wrapper to clustalo. It takes two sequence profiles and produces a combined output alignment.

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.

Algorithm

Clustal-Omega uses HMMs for the alignment engine, based on the HHalign package from Johannes Soeding [1]. Guide trees are optionally made using mBed [2] which can cluster very large numbers of sequences in O(N*log(N)) time. Multiple alignment then proceeds by aligning larger and larger alignments using HHalign, following the clustering given by the guide tree.

Usage

Here is a sample session with eomegapp 


% eomegapp ../data/op2.ali  
Profile with profile (ClustalO wrapper)
(aligned) protein output sequence set [op1.aln]: 
WARNING: This is a beta version of Clustal Omega, for protein only.

Go to the input files for this example
Go to the output files for this example

Command line arguments 

Profile with profile (ClustalO wrapper)
Version: EMBOSS:6.4.0.0

   Standard (Mandatory) qualifiers:
  [-aprofile]          infile     Pre-aligned multiple sequence file (aligned
                                  columns will be kept fixed)
  [-bprofile]          infile     Pre-aligned multiple sequence file (aligned
                                  columns will be kept fixed)
  [-outseq]            seqoutset  [.] (Aligned) protein
                                  sequence set filename and optional format
                                  (output USA)

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -indist             infile     Pairwise distance matrix input file (skips
                                  distance computation)
   -inguide            infile     Guide tree input file (skips distance
                                  computation and guide tree clustering step)
   -dealign            toggle     [N] Dealign input sequences
   -mbed               toggle     [N] Fast, Mbed-like clustering for guide
                                  tree calculation
   -intermbed          toggle     [N] Fast, Mbed-like clustering for guide
                                  tree calculation
   -maxiterations      integer    [0] Number of (combined guide tree/HMM)
                                  iterations (Integer from 0 to 2000000000)
   -maxgiterations     integer    [2000000000] Maximum guide tree iterations
                                  (Integer from 0 to 2000000000)
   -maxhiterations     integer    [2000000000] Maximum number of HMM
                                  iterations (Integer from 0 to 2000000000)
   -maxseqs            integer    [2000000000] Maximum number of sequences
                                  (Integer from 2 to 2000000000)
   -maxlenseq          integer    [2000000000] Maximum length of sequence
                                  (Integer from 1 to 2000000000)
   -self               toggle     [N] Set options automatically (might
                                  overwrite some options
   -outdist            outfile    [*.eomegapp] Pairwise distance matrix output
                                  file
   -outguide           outfile    [*.eomegapp] Guide tree output file

   Associated qualifiers:

   "-outseq" associated qualifiers
   -osformat3          string     Output seq format
   -osextension3       string     File name extension
   -osname3            string     Base file name
   -osdirectory3       string     Output directory
   -osdbname3          string     Database name to add
   -ossingle3          boolean    Separate file for each entry
   -oufo3              string     UFO features
   -offormat3          string     Features format
   -ofname3            string     Features file name
   -ofdirectory3       string     Output directory

   "-outdist" associated qualifiers
   -odirectory         string     Output directory

   "-outguide" associated qualifiers
   -odirectory         string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to 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 and exit. 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 dying program messages
   -version            boolean    Report version number and exit

Qualifier Type Description Allowed values Default
Standard (Mandatory) qualifiers
[-aprofile]
(Parameter 1)		 infile Pre-aligned multiple sequence file (aligned columns will be kept fixed) Input file Required
[-bprofile]
(Parameter 2)		 infile Pre-aligned multiple sequence file (aligned columns will be kept fixed) Input file Required
[-outseq]
(Parameter 3)		 seqoutset (Aligned) protein sequence set filename and optional format (output USA) Writeable sequences <*>.format
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
-indist infile Pairwise distance matrix input file (skips distance computation) Input file Required
-inguide 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
-mbed toggle Fast, Mbed-like clustering for guide tree calculation Toggle value Yes/No No
-intermbed toggle Fast, Mbed-like clustering for guide tree calculation Toggle value Yes/No No
-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
-outdist outfile Pairwise distance matrix output file Output file <*>.eomegapp
-outguide outfile Guide tree output file Output file <*>.eomegapp
Associated qualifiers
"-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  
"-outdist" associated outfile qualifiers
-odirectory string Output directory Any string  
"-outguide" 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

Input file format

eomegapp reads two pre-aligned sequence file using native Clustal-OMega input processing (so EMBOSS sees this as a text input file) and optional distance and guide tree files.

Input files for usage example

File: op1.ali

>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

File: op2.ali

>OPSD_CAMHU O18312 Rhodopsin (Fragment)
-----------------------------------LHMIHLHWYQYPPMNPMMYPLLLIF
MLFTGILCLAGNFVTIWVFMNTKSLRTPANLLVVNLAMSDFLMMFTMFPPMMVTCYYHTW
TLGPTFCQVYAFLGNLCGCASIWTMVFITFDRYNVIVKGVAGEPLSTKKASLWILSVWVL
STAWCIAPFFGWNHYVPEGNLTGCGTDYLSEDI--LSRSYLYIYSTW-VYFLPLAITIYC
YVFIIKAVAAHEKGMRDQAKKMGIKSLRNEEAQKTSAECRLAKNAMTTVALWFIAWTPCL
LINWVGM-FARSYLSPVYTIWGYVFAKANAVYNPIVYAIS--------------------
-----------------------------
>OPSD_CAMLU O16017 Rhodopsin (Fragment)
-----------------------------------LHMIHLHWYQYPPMNPMMYPLLLVF
MLITGILCLAGNFVTIWVFMNTKSLRTPANLLVVNLAMSDFLMMFTMFPPMMITCYYHTW
TLGATFCEVYAFLGNLCGCASIWTMVFITFDRYNVIVKGVAGEPLSTKKASLWILTVWVL
SFTWCVAPFFGWNRYVPEGNLTGCGTDYLSEDI--LSRSYLYIYSTW-VYFLPLAITIYC
YVFIIKAVAAHEKGMRDQAKKMGIKSLRNEEAQKTSAECRLAKIAMTTVALWFIAWTPYL
LINWVGM-FARSYLSPVYTIWGYVFAKANAVYNPIVYAIS--------------------
-----------------------------
>OPSD_CAMMA O18315 Rhodopsin (Fragment)
-----------------------------------LHMIHLHWYQYPPMNPMMYPLLLVF
MLITGILCLAGNFVTIWVFMNTKSLRTPANLLVVNLAMSDFLMMFTMFPPMMVTCYYHTW
TLGATFCQVYAFLGNLCGCASIWTMVFITFDRYNVIVKGVAGEPLSTKKASLWILTIWIL
SITWCIAPFFGWNRYVPEGN-TGCGTDYLSEDI--LSRSYLYIYSTW-VYFLPLAITIYC
HVFIIKAVAAHEKGMRDQAKKMGIKSLRNEEAQKTSAECRLAKIAMTTVALWFIAWTPYL
LINWVGM-FARSYLSPVYTIWGYVFAKANAVYNPIVYAIS--------------------
-----------------------------
>OPSD_CAMSC O16018 Rhodopsin (Fragment)
-----------------------------------LHMIHLHWYQYPPMNPMMYPLLLIF
MFITGIPCLAGNFVTIWVFMTTKSLRSPANLLVVNLAMSDFLMMFTMFPPMMITCYYHTW
TLGPTFCQVYAFLGNLFGCTSIWTMVFITFDRYNVIVKGVAGEPLSNKKAALWILSAWVL
SFSWCSAPFFGWNRYVPEGNLTGCGTDYLSEDA--LSRSYLYVYSVW-VYFLPLLITIYC
YVFIIKAVAAHEKGMRDQAKKMGIKSLRNEEAQKTSAECRLAKIAMTTVALWFIAWTPYL
LINWVGM-FARSYLSPVYTIWGYVFAKANAVYNPIVYAIS--------------------
-----------------------------
>OPSD_CANFA P32308 Rhodopsin
-----------------MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAY
MFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYF
VFGPTGCNVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVM
ALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEINNESF-VIYMFVVHFAIPMIVIFFC
YGQLVFTVKEAAAQQQ-------------ESATTQKAEKEVTRMVIIMVIAFLICWVPYA
SVAFYIFTHQGSDFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMIT---TLCCGKN
PLGDDEAS---ASASKT---ETSQVAPA-
>OPSD_CARAU P32309 Rhodopsin
-----------------MNGTEGDMFYVPMSNATGIVRSPYDYPQYYLVAPWAYACLAAY
MFFLIITGFPVNFLTLYVTIEHKKLRTPLNYILLNLAISDLFMVFGGFTTTMYTSLHGYF
VFGRVGCNPEGFFATLGGEMGLWSLVVLAFERWMVVCKPVSNFRFGENHAIMGVVFTWFM
ACTCAVPPLVGWSRYIPEGMQCSCGVDYYTRPQAYNNESF-VIYMFIVHFIIPLIVIFFC
YGRLVCTVKEAAAQHE-------------ESETTQRAEREVTRMVVIMVIGFLICWIPYA
SVAWYIFTHQGSEFGPVFMTLPAFFAKTAAVYNPCIYICMNKQFRHCMIT---TLCCGKN
PFEEEEGASTTASKTEASSVSSSSVSPA-
>OPSD_CATBO Q17296 Rhodopsin
MMSIASGPSHAAYTWTAQGGGFGNQTVVDKVPPEMLHLVDAHWYQFPPMNPLWHAILGFV


  [Part of this file has been deleted for brevity]

YGRLLCAVKEAAAAQQ-------------ESETTQRSEKEVSRMVVLMVIGFLVCWLPYA
STAWWIFCNQGSEFGPVFMTIPAFFAKSSAIYNPMIYICMNKQFRHCMI-----------
-----------------------------
>OPSD_CORAU Q90305 Rhodopsin (Fragment)
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
-----------------------CGIDYYTRAPGYNNESF-VIYMFIVHFLIPLFIISFC
YGNLLCAVKAAAAAQE-------------ESETTQRAEREVTRMVIMMVISYLVSWVPYA
SVAWYIFSNQGSEFGPVFMTIPAFFAKSSALYNPLIYVLMNKQFRHCM------------
-----------------------------
>OPSD_COTBO O42307 Rhodopsin (Fragment)
----------------------------------------------YLVNPAAYAALGAY
MFLLILIGFPINFLTLYVTLEHKKLRTPLNYILLNLAVGNLFMVLGGFTTTMYTSMHGYF
VLGRLGCNLEGFFATLGGEIALWSLVVLAIERWIVVCKPISKFRFTEDHAIMGLAFSWVM
GLACAVPPLVGWSRYIPEGMKCSCGVDYYTRAEGFNNESF-VIYMFIVHFLIPLSVIFFC
YGRLLCAVKEAAAAQQ-------------ESETTQRAEKEVSRMVVIMVIGFLVCWLPYA
SVAWWIFCNQGSDFGPIFMTLPSFFAKRPAIYNPMIYICMNKQFRHCMI-----------
-----------------------------
>OPSD_COTGR O42328 Rhodopsin (Fragment)
----------------------------------------------YLVNPAAYAAPGAY
MFLLILVGFPVNFLTLYVTLEHKKLRTPLNYILLNLAVADLFMVLGGFTTTMYTSMHGYF
VLGRLGCNLEGFFATLGGEIALWSLVVLAIERWIVVCKPISNFRFTEDHAIMGLAFSWVM
ALTCAVPPLVGWSRYIPEGMQCSCGVDYYTRAEGFNNESF-VIYMFIVHFLIPLSNNFFC
YGRLLCAVKEAAAAQQ-------------ESETTQRAEREVSRMVVMMVVSFLMCWLPYA
SVAWYIFCNQGSEFGPIFMTLPAFFAKSSAIYNPLIYICMNKHVRHCMI-----------
-----------------------------
>OPSD_COTIN O42330 Rhodopsin (Fragment)
----------------------------------------------YLVNPAAYAALGAY
MFLLILIGFPVNFLTLYVTIEHKKLRTPLNYILLNLAVANLFMVLGGFTTTMYTSMHGYF
VLGRLGCNLEGFFATMGGEIALWSLVVLAIERWIVVCKPISNFRFTEDHAIMGLAFTWVM
ALSCAVPPLVGWSRYIPEGMQCSCGVDYYTRAEGFNNESF-VIYMFIVHFLTPLIIISFC
YGRLLCAVKEAAAAQQ-------------ESETTQRAEREVSRMVVMMVISFLMCWLPYA
SVAWYIFCNQGSEFGPIFMTLPAFFAKSSAIYNPLIYICMNKQFRHCMI-----------
-----------------------------
>OPSD_COTKE Q90373 Rhodopsin (Fragment)
----------------------------------------------YLVSPAGYAALGAY
MFLLILVGFPVNFLTLYVTLEHKKLRTPLNYILLNLAVADLFMVLGGFTTTMYTSMHGYF
VLGRLGCNLEGFFVTLGGEIALWSLVVLAIERWIGVFKSIRNFRFTEDHAIMGLGFSWVM
AATCAVPPLVGWLRYIPEGMQCSCGVDYYTRAEGFNNESF-VIYMFIVHFLIPLIVIFFC
YGRLLCAVKEAAAAQQ-------------ESETTQRAEKEVSRMVVIMVIGYLVCWLPYA
SVAWWIFCNQGSEFGPIFMTLPAFFAKSPAIYNPLIYICMNKQFPHCMI-----------
-----------------------------
>OPSD_CRIGR P28681 Rhodopsin
-----------------MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAY
MFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYF
VFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVICKPMSNFRFGENHAIMGVVFTWIM
ALACAAPPLVGWSRYIPEGMQCSCGVDYYTLKPEVNNESF-VIYMFVVHFTIPLIVIFFC
YGQLVFTVKEAAAQQQ-------------ESATTQKAEKEVTRMVILMVVFFLICWFPYA
GVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLT---TLCCGKN
ILGDDEAS---ATASKT---ETSQVAPA-

Output file format

eomegapp writes alignments using the default Clustal-Omega output.

Output files for usage example

File: op1.aln

>OPSD_ABYKO O42294 Rhodopsin (Fragment)
----------------------------------------------------------YL
VNPAAYAALGAYMFLLILIGFP---INFLTLYVTLEHKKLRTPLNYILLNLAVANLFMVL
GGFTTTMYTSMHGYFVLGRLGCNLEAFFATLGGEIALWSLVVLAIERWIVVCKPISNFRF
TEDHAIMGLAFTWVMALACAVPPLVGWSRYIPEGMQCSCGVDYYTRAEGFNNESF-VIYM
FIVHFLIPLSVIFFCYGRLLCAVKEAPAAQQE-------------SETTQRAEKEVSRMV
VIMVIGFLVCWLPYASVAWWIFCNQGSDFGPIFMTLPSFFAKSAAIYNPMIYICMNKQFR
HCMI----------------------------------------
>OPSD_AMBTI Q90245 Rhodopsin
-----------------MNGTEGPNFYV-------PFSNKSGVVRSPFEYP-----QYYL
AEPWQYSVLAAYMFLLILLGFP---VNFLTLYVTIQHKKLRTPLNYILLNLAFANHFMVF
GGFPVTMYSSMHGYFVFGQTGCYIEGFFATMGGEIALWSLVVLAIERYVVVCKPMSNFRF
GENHAIMGVMMTWIMALACAAPPLFGWSRYIPEGMQCSCGVDYYTLKPEVNNESF-VIYM
FLVHFTIPLMIIFFCYGRLVCTVKEAAAQQQE-------------SATTQKAEKEVTRMV
IIMVVAFLICWVPYASVAFYIFSNQGTDFGPIFMTVPAFFAKSSAIYNPVIYIVLNKQFR
NCMIT---TICCGKNPFGDDETTSAATSKTEASSVSSSQVSPA-
>OPSD_ANOCA P41591 Rhodopsin
-----------------MNGTEGQNFYV-------PMSNKTGVVRNPFEYP-----QYYL
ADPWQFSALAAYMFLLILLGFP---INFLTLFVTIQHKKLRTPLNYILLNLAVANLFMVL
MGFTTTMYTSMNGYFIFGTVGCNIEGFFATLGGEMGLWSLVVLAVERYVVICKPMSNFRF
GETHALIGVSCTWIMALACAGPPLLGWSRYIPEGMQCSCGVDYYTPTPEVHNESF-VIYM
FLVHFVTPLTIIFFCYGRLVCTVKAAAAQQQE-------------SATTQKAEREVTRMV
VIMVISFLVCWVPYASVAFYIFTHQGSDFGPVFMTIPAFFAKSSAIYNPVIYILMNKQFR
NCMIM---TLCCGKNPLGDEETSAG--TKTETSTVSTSQVSPA-
>OPSD_APIME Q17053 Rhodopsin, long-wavelength (Opsin, green-sensitive)
-----------------MIAVSGPSYEAFSYGGQARFNNQTVVDKVPPDMLHLIDANWYQ
YPPLNPMWHGILGFVIGMLGFVSAMGNGMVVYIFLSTKSLRTPSNLFVINLAISNFLMMF
CMSPPMVINCYYETWVLGPLFCQIYAMLGSLFGCGSIWTMTMIAFDRYNVIVKGLSGKPL
SINGALIRIIAIWLFSLGWTIAPMFGWNRYVPEGNMTACGTDYFNRGL--LSASY-LVCY
GIWVYFVPLFLIIYSYWFIIQAVAAHEKNMREQAKKMNVASLRSSENQNTSAECKLAKVA
LMTISLWFMAWTPYLVINFSGIF-NLVKISPLFTIWGSLFAKANAVYNPIVYGISHPKYR
AALFAKFPSLACAAEPSSDAVSTTSGTTTVTD-----NEKSNA-
>OPSD_ASTFA P41590 Rhodopsin
-----------------MNGTEGPYFYV-------PMSNATGVVRSPYEYP-----QYYL
APPWAYACLAAYMFFLILVGFP---VNFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVF
GGFTTTMYTSLNGYFVFGRLGCNLEGFFATFGGINSLWCLVVLSIERWVVVCKPMSNFRF
GENHAIMGVAFTWFMALACTVPPLVGWSRYIPEGMQCSCGIDYYTRAEGFNNESF-VIYM
FVVHFLTPLFVITFCYGRLVCTVKEAAAQQQE-------------SETTQRAEREVTRMV
ILMFIAYLVCWLPYASVSWWIFTNQGSEFGPIFMTVPAFFAKSSSIYNPVIYICLNKQFR
HCMIT---TLCCGKNPFEEEEGASTTASKTEASSVSSVSPA---
>OPSD_ATHBO Q9YGZ1 Rhodopsin
-----------------MNGTEGPYFYI-------PMLNTTGVVRSPYEYP-----QYYL
VNPAAYAVLGAYMFFLILVGFP---INFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVF
GGFTTTIYTSMHGYFVLGRLGCNVEGFSATLGGEIALWSLVVLAIERWVVVCKPISNFRF
GENHAIMGVAFTWFMAAACAVPPLFGWSRYIPEGMQCSCGIDYYTRAEGFNNESF-VIYM
FTCHFCIPLMVVFFCYGRLVCAVKEAAAAQQE-------------SETTQRAEREVTRMV
IIMVVSFLVSWVPYASVAWYIFTHQGSEFGPLFMTIPAFFAKSSSIYNPMIYICMNKQFR
HCMIT---TLCCGKNPFEEEEGASSTASKTEASSVSSSSVSPA-
>OPSD_BATMU O42300 Rhodopsin (Fragment)
----------------------------------------------------------YL


  [Part of this file has been deleted for brevity]

FTVHFLIPLSVIFFCYGRLLCAVKEAAAAQQ-------------ESETTQRSEKEVSRMV
VLMVIGFLVCWLPYASTAWWIFCNQGSEFGPVFMTIPAFFAKSSAIYNPMIYICMNKQFR
HCMI----------------------------------------
>OPSD_CORAU Q90305 Rhodopsin (Fragment)
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
--------------------------------------CGIDYYTRAPGYNNESF-VIYM
FIVHFLIPLFIISFCYGNLLCAVKAAAAAQE-------------ESETTQRAEREVTRMV
IMMVISYLVSWVPYASVAWYIFSNQGSEFGPVFMTIPAFFAKSSALYNPLIYVLMNKQFR
HCM-----------------------------------------
>OPSD_COTBO O42307 Rhodopsin (Fragment)
----------------------------------------------------------YL
VNPAAYAALGAYMFLLILIGFP---INFLTLYVTLEHKKLRTPLNYILLNLAVGNLFMVL
GGFTTTMYTSMHGYFVLGRLGCNLEGFFATLGGEIALWSLVVLAIERWIVVCKPISKFRF
TEDHAIMGLAFSWVMGLACAVPPLVGWSRYIPEGMKCSCGVDYYTRAEGFNNESF-VIYM
FIVHFLIPLSVIFFCYGRLLCAVKEAAAAQQ-------------ESETTQRAEKEVSRMV
VIMVIGFLVCWLPYASVAWWIFCNQGSDFGPIFMTLPSFFAKRPAIYNPMIYICMNKQFR
HCMI----------------------------------------
>OPSD_COTGR O42328 Rhodopsin (Fragment)
----------------------------------------------------------YL
VNPAAYAAPGAYMFLLILVGFP---VNFLTLYVTLEHKKLRTPLNYILLNLAVADLFMVL
GGFTTTMYTSMHGYFVLGRLGCNLEGFFATLGGEIALWSLVVLAIERWIVVCKPISNFRF
TEDHAIMGLAFSWVMALTCAVPPLVGWSRYIPEGMQCSCGVDYYTRAEGFNNESF-VIYM
FIVHFLIPLSNNFFCYGRLLCAVKEAAAAQQ-------------ESETTQRAEREVSRMV
VMMVVSFLMCWLPYASVAWYIFCNQGSEFGPIFMTLPAFFAKSSAIYNPLIYICMNKHVR
HCMI----------------------------------------
>OPSD_COTIN O42330 Rhodopsin (Fragment)
----------------------------------------------------------YL
VNPAAYAALGAYMFLLILIGFP---VNFLTLYVTIEHKKLRTPLNYILLNLAVANLFMVL
GGFTTTMYTSMHGYFVLGRLGCNLEGFFATMGGEIALWSLVVLAIERWIVVCKPISNFRF
TEDHAIMGLAFTWVMALSCAVPPLVGWSRYIPEGMQCSCGVDYYTRAEGFNNESF-VIYM
FIVHFLTPLIIISFCYGRLLCAVKEAAAAQQ-------------ESETTQRAEREVSRMV
VMMVISFLMCWLPYASVAWYIFCNQGSEFGPIFMTLPAFFAKSSAIYNPLIYICMNKQFR
HCMI----------------------------------------
>OPSD_COTKE Q90373 Rhodopsin (Fragment)
----------------------------------------------------------YL
VSPAGYAALGAYMFLLILVGFP---VNFLTLYVTLEHKKLRTPLNYILLNLAVADLFMVL
GGFTTTMYTSMHGYFVLGRLGCNLEGFFVTLGGEIALWSLVVLAIERWIGVFKSIRNFRF
TEDHAIMGLGFSWVMAATCAVPPLVGWLRYIPEGMQCSCGVDYYTRAEGFNNESF-VIYM
FIVHFLIPLIVIFFCYGRLLCAVKEAAAAQQ-------------ESETTQRAEKEVSRMV
VIMVIGYLVCWLPYASVAWWIFCNQGSEFGPIFMTLPAFFAKSPAIYNPLIYICMNKQFP
HCMI----------------------------------------
>OPSD_CRIGR P28681 Rhodopsin
-----------------MNGTEGPNFYV-------PFSNATGVVRSPFEYP-----QYYL
AEPWQFSMLAAYMFLLIVLGFP---INFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVF
GGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVICKPMSNFRF
GENHAIMGVVFTWIMALACAAPPLVGWSRYIPEGMQCSCGVDYYTLKPEVNNESF-VIYM
FVVHFTIPLIVIFFCYGQLVFTVKEAAAQQQ-------------ESATTQKAEKEVTRMV
ILMVVFFLICWFPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFR
NCMLT---TLCCGKNILGDDEAS---ATASKT---ETSQVAPA-

Data files

None.

Notes

None.

References

[1] Johannes Soding (2005) Protein homology detection by HMM-HMM comparison. Bioinformatics 21 (7): 951–960.

[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.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with status 0.

Known bugs

None.

See also

Program name Description
edialign Local multiple alignment of sequences
emma Multiple sequence alignment (ClustalW wrapper)
eomega Multiple sequence alignment (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

Author(s)

Alan Bleasby
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.

History

Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

Comments

None