unix % emma
Multiple alignment program - interface to ClustalW program
Input sequence: OPS2_*.fasta
Output sequence [OPS2_*drome.aln]: OPS2_*.aln
Output file [OPS2_*drome.dnd]: OPS2_*.dnd
..clustalw -infile=21665A -outfile=21665B -align
-type=protein -output=gcg -pwmatrix=blosum -pwgapopen=10.000
-pwgapext=0.100 -newtree=21665C -matrix=blosum -gapopen=10.000
-gapext=5.000 -gapdist=8 -hgapresidues=GPSNDQEKR -maxdiv=30..
CLUSTAL W (1.74) Multiple Sequence Alignments
Sequence type explicitly set to Protein
Sequence format is Pearson
Sequence 1: OPS2_*DROME 381 aa
Sequence 2: OPS2_*DROPS 381 aa
Sequence 3: OPS2_*HEMSA 377 aa
Sequence 4: OPS2_*LIMPO 376 aa
Sequence 5: OPS2_*PATYE 399 aa
Sequence 6: OPS2_*SCHGR 380 aa
Start of Pairwise alignments
Aligning...
Sequences (1:2) Aligned. Score: 91
Sequences (1:3) Aligned. Score: 37
Sequences (1:4) Aligned. Score: 48
Sequences (1:5) Aligned. Score: 20
Sequences (1:6) Aligned. Score: 32
Sequences (2:3) Aligned. Score: 37
Sequences (2:4) Aligned. Score: 48
Sequences (2:5) Aligned. Score: 22
Sequences (2:6) Aligned. Score: 31
Sequences (3:4) Aligned. Score: 40
Sequences (3:5) Aligned. Score: 23
Sequences (3:6) Aligned. Score: 32
Sequences (4:5) Aligned. Score: 20
Sequences (4:6) Aligned. Score: 34
Sequences (5:6) Aligned. Score: 18
Guide tree file created: [21665C]
Start of Multiple Alignment
There are 5 groups
Aligning...
Group 1: Sequences: 2 Score:6084
Group 2: Sequences: 3 Score:3046
Group 3: Sequences: 4 Score:2772
Group 4: Sequences: 5 Score:2489
Group 5: Delayed
Sequence:5 Score:2819
Alignment Score 11778
GCG-Alignment file created [21665B]
We have aligned OPS2_* sequences from two fruit fly species, two crab species, locust and scallop. Let's see what emma made of them:
unix % more OPS2_*.aln
>OPS2_*DROME MERSHLPETPFDLAHSGPRFQAQSSGNGSVLD-NVLPDMAHLVNPYWSRFAPMDPMMSKI LGLFTLAIMIISCCGNGVVVYIFGGTKSLRTPANLLVLNLAFSDFCMMASQSPVMIINFY Y-ETWVLGPLWCDIYAGCGSLFGCVSIWSMCMIAFDRYNVIVKGINGTPMTIKTSIMKIL FIWMMAVFWTVMPLIGWSAYVPEGNLTACSIDYMTRMWNPRSYLITYSLFVYYTPLFLIC YSYWFIIAAVAAHEKAMREQAKKMNVKSLRSSEDCDK-SAEGKLAKVALTTISLWFMAWT PYLVICYFGLFKIDG-LTPLTTIWGATFAKTSAVYNPIVYGISHPKYRIVLKEKCPMCVF GNTDEPKPDAPASDTETTSEADSKA----------------------------------- --------------------------- >OPS2_*DROPS MERSLLPEPPLAMALLGPRFEAQTGGNRSVLD-NVLPDMAPLVNPHWSRFAPMDPTMSKI LGLFTLVILIISCCGNGVVVYIFGGTKSLRTPANLLVLNLAFSDFCMMASQSPVMIINFY Y-ETWVLGPLWCDIYAACGSLFGCVSIWSMCMIAFDRYNVIVKGINGTPMTIKTSIMKIA FIWMMAVFWTIMPLIGWSSYVPEGNLTACSIDYMTRQWNPRSYLITYSLFVYYTPLFMIC YSYWFIIATVAAHEKAMRDQAKKMNVKSLRSSEDCDK-SAENKLAKVALTTISLWFMAWT PYLIICYFGLFKIDG-LTPLTTIWGATFAKTSAVYNPIVYGISHPNDRLVLKEKCPMCVC GTTDEPKPDAPPSDTETTSEAESKD----------------------------------- --------------------------- >OPS2_*LIMPO ----------MANQLSYSSLGWPYQPNASVVD-TMPKEMLYMIHEHWYAFPPMNPLWYSI LGVAMIILGIICVLGNGMVIYLMMTTKSLRTPTNLLVVNLAFSDFCMMAFMMPTMASNCF A-ETWILGPFMCEVYGMAGSLFGCASIWSMVMITLDRYNVIVRGMAAAPLTHKKATLLLL FVWIWSGGWTILPFFGWSRYVPEGNLTSCTVDYLTKDWSSASYVIIYGLAVYFLPLITMI YCYFFIVHAVAEHEKQLREQAKKMNVASLRANADQQKQSAECRLAKVAMMTVGLWFMAWT PYLIIAWAGVFSSGTRLTPLATIWGSVFAKANSCYNPIVYGISHPRYKAALYQRFPSLAC GSGESGSDVKSEASATMTMEEKPKSPEA-------------------------------- --------------------------- >OPS2_*HEMSA ---MTNATGPQMAYYGAASMDFGYPEGVSIVD-FVRPEIKPYVHQHWYNYPPVNPMWHYL LGVIYLFLGTVSIFGNGLVIYLFNKSAALRTPANILVVNLALSDLIMLTTNVPFFTYNCF SGGVWMFSPQYCEIYACLGAITGVCSIWLLCMISFDRYNIICNGFNGPKLTTGKAVVFAL ISWVIAIGCALPPFFGWGNYILEGILDSCSYDYLTQDFNTFSYNIFIFVFDYFLPAAIIV FSYVFIVKAIFAHEAAMRAQAKKMNVSTLRSNEADAQ-RAEIRIAKTALVNVSLWFICWT PYALISLKGVMGDTSGITPLVSTLPALLAKSCSCYNPFVYAISHPKYRLAITQHLPWFCV HETETKSNDDSQSNSTVAQDKA-------------------------------------- --------------------------- >OPS2_*SCHGR ------MVNTTDFYPVPAAMAYESSVGLPLLGWNVPTEHLDLVHPHWRSFQVPNKYWHFG LAFVYFMLMCMSSLGNGIVLWIYATTKSIRTPSNMFIVNLALFDVLMLLEMPMLVVSSLF Y-QRPVGWELGCDIYAALGSVAGIGSAINNAAIAFDRYRTISCPIDGRLTQGQVLALIAG TWVWTLPFTLMPLLRIWSRFTAEGFLTTCSFDYLTDDEDTKVFVGCIFAWSYAFPLCLIC CFYYRLIGAVREHEKMLRDQAKKMNVKSLQSNADTEAQSAEIRIAKVALTIFFLFLCSWT PYAVVAMIGAFGNRAALTPLSTMIPAVTAKIVSCIDPWVYAINHPRFRAEVQKRMKWLHL GEDARSSKSDTSSTATDRTVGNVSASA--------------------------------- --------------------------- >OPS2_*PATYE ---------------------------------------MPFPLNRTDTALVISPSEFRI IGIFISICCIIGVLGNLLIIIVFAKRRSVRRPINFFVLNLAVSDLIVALLGYPMTAASAF S-NRWIFDNIGCKIYAFLCFNSGVISIMTHAALSFCRYIIICQYGYRKKITQTTVLRTLF SIWSFAMFWTLSPLFGWSSYVIEVVPVSCSVNWYGHGLGDVSYTISVIVAVYVFPLSIIV FSYGMIL-----QEKVCKDSRKNGIRAQQRYTPRFIQ-DIEQRVTFISFLMMAAFMVAWT PYAIMSALAIGSFNV--ENSFAALPTLFAKASCAYNPFIYAFTNANFRDTVVEIMAPWTT RRVGVSTLPWPQVTYYPRRRTSAVNTTDIEFPDDNIFIVNSSVNGPTVKREKIVQRNPIN VRLGIKIEPRDSRAATENTFTADFSVI
The sequences are very similar, but there are some differences - note the gaps that have been inserted. Also note that since this is a global alignment algorithm, gaps have been inserted to make all the sequences the same length.
Differences in alignment can be very difficult to see in this format. The program Prettyplot can enhance visualisation of your results, by aligning the sequences on top of one another.