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%