Version 1.0
This is the first release of the program.
If you observe a bug or suspicious behavior, or get a nonsense result, please
send us a note,
containing the query alignment and the parameters you've used. Thank you.
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GDE alignment format
The GDE alignment format is one of the standard alignment formats. Popular programs for sequence alignment,
e.g. ClustalW, can save alignment in this format. In this format, all letters indicating amino
acids are in lower case, gaps are indicated by dashes. Sequences are placed one after another, the name of
each sequence is placed onto a separate line and begins with ‘%’. The sequence
begins in the next line and may be broken into several lines. Thus the alignment looks like this:
%EC_RbsR
-------------------------matmkdvarlagvststvshvinkd---rfvseai
takveaaikelnyap---salarslklnqthtigmlitastn-----pfyselvrgvers
cfergyslvlcntegd-eqrmnrnletlmqk-rvdgllllctethqpsreimqryptvpt
--vmmdw--apfdgdsdliqdnsllggdlatqylidkghtr-iacitg-pldktparlr-
-----legyraamkraglnipdgyevtg---dfefnggfdamrqllshp--lrpqavftg
ndamavgvyqalyqae-lqvpqdiavigyddie---lasfmtpplttihqpkdelgelai
dvlihritqpt------lqqqrlqltpilmergsa------------------------
%Pp_RbsR
-------------------------matikdvaalagisyttvshvlnkt---rpvseqv
rlkveaaiieldyvp---savarslkarstatigllvpnsvn-----pyfaelargieda
cerngycvilcnsddn-pqkqrsylrvllek-ridglvvasvgqdd---dllqslasvrt
pmvivdr--elegvdadlvridheqgaylatrhllelghrd-vayigg-paetgvtqlr-
-----lsgfrramaeagapvpgsrvlhc---dftspgghaaaaqvleg---krpsaifag
ndmigfgvlraaaern-isvpgelsvigfddie---lsryvypslttvgqsirelgesaa
sllltriatprqg----aaeqrivaprivlrestgprpdlfndy---------------
%BS_RbsR
-------------------------matikdvagaagvsvatvsrnlndn---gyvheet
rtrviaamaklnyyp---nevarslykresrliglllpditn-----pffpqlargaede
lnregyrlifgnsdee-lkkeleylqtfkqn-hvagiiaat------nypdleeysgmny
pvvfldr--tleg-apsvss-dgytgvklaaqaiihgksqr-itllrg-pahlptaqdr-
-----fngaleilkqa--evdfqvieta---sfsikdaqsmakelfasy--patdgvias
ndiqaaavlhealrrg-knvpediqiigyddip---qsgllfpplstikqpaydmgkeaa
klllgiikkqp------laetaiqmpvtyigrkttrked--------------------
%SACR_LACLA
-------------------------mikledvankagvsvttvsrvinrk---gylsdat
iskvekamqdlhyip---naaarslqgkslkliglvfptikn-----ifyaeliekieqa
lfirgykamlattehd-eqkerdylalllsn-qvdgiiygs------hnlkahdyiaiea
pivafdr--lltp-ettvvssdnfeggilatkalinsgskk-iaiftgndntnsptylr-
-----rdgyllelern--qlkthiikip---sqwtllrkkveikkilen--ndfdgvfct
ddltailvkdlas-----nlkkslnvvgfdgte---fienyypnlttikqpindlaellv
dliirkidgd-------nidityqlpvqlhygid-------------------------
back to input format rules
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