Question: Clustal Omega usage: Where is the score summary output?
1
dssouzadan • 30 wrote:
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%