                                  eomegapp



Wiki

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   http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.

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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]:


   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:6.6.0.0

   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:
   -indistfile         infile     Pairwise distance matrix input file (skips
                                  distance computation)
   -inguidefile        infile     Guide tree input file (skips distance
                                  computation and guide tree clustering step)
   -dealign            toggle     [N] Dealign input sequences
   -cluster            menu       [mbed] Method (Values: mbed (mBED method);
                                  full (Full slow method); iter (Iteration
                                  used full slower method))
   -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
   -outformat          menu       [fasta] Format (Values: fasta (FASTA);
                                  clustal (Aln clustal); msf (MSF); phylip
                                  (Phylip); selex (Selex); stockholm
                                  (Stockholm); vienna (ViennaRNA))
   -outdistfile        outfile    [*.eomegapp] Pairwise distance matrix output
                                  file, only available in cluster mode 'full'
   -outguidefile       outfile    [*.eomegapp] Guide tree output file
   -log                toggle     [N] Log progress to standard output if not
                                  used for output

   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

   "-outdistfile" associated qualifiers
   -odirectory         string     Output directory

   "-outguidefile" 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


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): 951aEUR"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: 111aEUR"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)
   eomegaps         Single sequence 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

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 (c) 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
