GDE alignment format |
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GDE alignment format is one of standard alignment formats. A popular program for sequence alignment,
Clustal, for example, 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, name of
each sequence is placed onto a separate line and begins with ‘%’. The sequence is placed afterwards
beginning on the next line and may be broken into several lines. Thus the alignment might look 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------------------------- |