Blocks finder

A program for automatic detection of aligned blocks in multiple protein alignment.

Paste your alignment in fasta-format here:

Or upload from file:

Sample alignment in fasta-format (A4_extra Pfam family seed):

>APLP2_RAT/42-204
GTGFAVAEPQIAMFCG....KLNMHVNIQTGKWEPDPTGTK...SCLGTKEEVLQYCQEI
YPELQITNVMEANQPVNIDSWCRRD...KKQCRSH...IVIPFKCLVGEFVSDVLLVPEN
CQFFHQERMEVCEKHQRWHTVVKEACLTE......GMTLYSYGMLLPCGVDQFHGTEYVC
CP
>A4_HUMAN/24-188
GNAGLLAEPQIAMFCG....RLNMHMNVQNGKWDSDPSGTK...TCIDTKEGILQYCQEV
YPELQITNVVEANQPVTIQNWCKRG...RKQCKTHP.HFVIPYRCLVGEFVSDALLVPDK
CKFLHQERMDVCETHLHWHTVAKETCSEK......STNLHDYGMLLPCGIDKFRGVEFVC
CP
>APLP1_HUMAN/46-211
GAAEAPGSAQVAGLCG....RLTLHRDLRTGRWEPDPQRSR...RCLRDPQRVLEYCRQM
YPELQIARVEQATQAIPMERWCGGS...RSGSCAHPHHQVVPFRCLPGEFVSEALLVPEG
CRFLHQERMDQCESSTRRHQEAQEACSSQ......GLILHGSGMLLPCGSDRFRGVEYVC
CP
>A4_CAEEL/28-196
SKRHEKFIPMVAFSCG....YRNQYMTEE.GSWKTDDERYA...TCFSGKLDILKYCRKA
YPSMNITNIVEYSHEVSISDWCREE...GSPCKWT..HSVRPYHCIDGEFHSEALQVPHD
CQFSHVNSRDQCNDYQHWKDEAGKQCKTKKSKGNKDMIVRSFAVLEPCALDMFTGVEFVC
CP
>A4_DROME/26-198
QAASPRWEPQIAVLCEAGQIYQPQYLSEE.GRWVTDLSKKTTGPTCLRDKMDLLDYCKKA
YPNRDITNIVESSHYQKIGGWCRQGALNAAKCKGSH.RWIKPFRCL.GPFQSDALLVPEG
CLFDHIHNASRCWPFVRWNQTGAAACQER......GMQMRSFAMLLPCGISVFSGVEFVC
CP


The program works slow - it takes 8 seconds to process alignment of 6 sequences of length 500.

The program's development is supported by Russian Foundation for Basic Research (grant 10-07-00685-a) and Ministry of Education and Science of the Russian Federation (State Contract No. 07.514.11.4006).