Clustal Omega usage: Where is the score summary output?
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6.8 years ago
dssouzadan ▴ 30

When I use the clustal omega I can't generate the score summary to evaluate the multiple alignment.

Using the --help command I saw that I can generate only the following alignment outputs:

--outfmt={a2m=fa[sta],clu[stal],msf,phy[lip],selex,st[ockholm],vie[nna]} MSA output file format (default: fasta)

The default output is in fasta format. So, there's no score table or summary output like ClustalW.

Is it correct to calculate the MSA percentage score using sum_of [*.: ocurrences] / MSA_align_length produced by the clustal output format (--outfmt=clu)?

or there are some parameter to generate the score file?

From the following MSA:

query                      -MKNTLLKLGVCVSLLGITPF--VSTISSVQAERTVEHKVIKNETGTISISQLNKNV---
gi|2984094                 ---------------MGGFLFFFLLVLFSFSSEYPKHV--------KETLRKITDRIYGV
gi|115023|sp|P10425|       MKKNTLLKVGLCVSLLGTTQF--VSTISSVQASQKVEQIVIKNETGTISISQLNKNV---
gi|115030|sp|P25910|       -MKTVFILIS---------------MLFPV---AVMAQK-SVKISDDISITQLSDKV---
gi|282554|pir||S25844      -------------------------------------M--------TVEVREVAE-----
                                                                            : :: .     

query                      -WVHTELGYFSG-EAVPSNGLVLNTSKGLVLVDSSWDDKLTKELIEMVEKKFKKRVTDVI
gi|2984094                 FGVYEQVSYENRG--FISNAYFYVADDGVLVVDALSTYKLGKELIESIRSVTNKPIRFLV
gi|115023|sp|P10425|       -WVHTELGYFNG-EAVPSNGLVLNTSKGLVLVDSSWDNKLTKELIEMVEKKFQKRVTDVI
gi|115030|sp|P25910|       -YTYVSLAEIEGWGMVPSNGMIVINNHQAALLDTPINDAQTEMLVNWVTDSLHAKVTTFI
gi|282554|pir||S25844      -GVYAYEQAPGGW--CVSNAGIVVGGDGALVVDTLSTIPRARRLAEWVDKLAAGPGRTVV
                             .:             **. .    .   ::*:       . * : : .        .:

query                      ITHAHADRIGGMKTLKERGIKAHSTALTAE------------LAKK---------NGYEE
gi|2984094                 VTHYHTDHFYGAKAFREVGAEVIAHEWAFDYI-SQPSSYNFFLARKKILKEHLEGTELTP
gi|115023|sp|P10425|       ITHAHADRIGGITALKERGIKAHSTALTAE------------LAKK---------SGYEE
gi|115030|sp|P25910|       PNHWHGDCIGGLGYLQRKGVQSYANQMTID------------LAKE---------KGLPV
gi|282554|pir||S25844      NTHFHGDHAFGNQVFAP-GTRIIAHEDMRSAMVTTGLAL-----TGLWPRVDWGEIELRP
                            .* * *   *   :   * .  :     .                              

query                      PLGDLQSVTNLKF----GNMKVETFYPGKGHTEDNIVVWLPQYQILAGGCLVKSASSKDL
gi|2984094                 PTITLTKNLNVYLQVGKEYKRFEVLHLCRAHTNGDIVVWIPDEKVLFSGDIVFDGRLPFL
gi|115023|sp|P10425|       PLGDLQTVTNLKF----GNTKVETFYPGKGHTEDNIVVWLPQYQILAGGCLVKSAEAKNL
gi|115030|sp|P25910|       PEHGFTDSLTVSL----DGMPLQCYYLGGGHATDNIVVWLPTENILFGGCMLKDNQATSI
gi|282554|pir||S25844      PNVTFRDRLTLH--VG--ERQVELICVGPAHTDHDVVVWLPEERVLFAGDVVMSGVTPFA
                           *   :    .:          .:      .*:  ::***:*  .:* .* :: .      

query                      GNVADAYVNEWSTSIENVLKRYGNINLVVPGHGEVGDRGLLLHTLDLLK-----------
gi|2984094                 GS---GNSRTWLVCLDEILKMKP--RILLPGHGEALIGEK--KIKEAVSWTRKYIKDLRE
gi|115023|sp|P10425|       GNVADAYVNEWSTSIENMLKRYRNINLVVPGHGKVGDKGLLLHTLDLLK-----------
gi|115030|sp|P25910|       GNISDADVTAWPKTLDKVKAKFPSARYVVPGHGDYGGTELIEHTKQIVN---QY----IE
gi|282554|pir||S25844      LF---GSVAGTLAALDRLAELEP--EVVVGGHGPVAGPEVIDANRDYLRWVQRLAADAVD
                                .        ::.:       . :: ***            : :            

query                      ------------------------------------------------------------
gi|2984094                 TIRKLYE--EGCDVECVRERINEELIKIDPSYAQVPVFFNVNPVNAYYVYFEIENEILMG
gi|115023|sp|P10425|       ------------------------------------------------------------
gi|115030|sp|P25910|       STSKP-------------------------------------------------------
gi|282554|pir||S25844      RRLTPLQAARRADLGAFAGLLDA---------------------ERLVANLHRAHEELLG
                                                                                       

query                      --------------------------
gi|2984094                 E-------------------------
gi|115023|sp|P10425|       --------------------------
gi|115030|sp|P25910|       --------------------------
gi|282554|pir||S25844      GHVRDAMEIFAELVAYNGGQLPTCLA
                                                    

Is it correct?:

sum_of [*.: ocurrences]: 69

MSA_alignment_length: 386

conservation percentage: 69/386 = 0,178756477 =~ 17,88%
alignment clustal omega • 4.0k views
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