Use this to find sequence similarity of your favorite protein in a database of proteins, for example, in the proteome of another organism. Alternative to the NCBI BLAST server, it can also be ran locally with the command line. Example sequence for BLAST.
>HSP70B MPVQQMTSMRSQSLAGAPVAPVKAGRAGVSRRGLAVSVRAEKVVGIDLGTTNSAVAAMEG GKPTIITNAEGGRTTPSVVAFTKTGDRLVGQIAKRQAVVNPENTFFSVKRFIGRRMSEVG SESTQVPYRVIEDGGNVKIKCPNAGKDFAPEEISAQVLRKLTEDAAKFLNDKVEKAVITV PAYFNDSQRQATKDAGKIAGLEVLRIINEPTAASLAYGFDKKANETILVFDLGGGTFDVS VLEVGDGVFEVLSTSGDTHLGGDDFDKRIVDFLADDFKKSEGIDLRKDRQALQRLTEAAE KAKIELSGMAQTSINLPFITATADGPKHIDTQLTRAKFEEMCNDLLERCKVPVQQALRDA KLSISDIQEVILVGGSTRIPAVQEIVRKLSGGKDPNVTVNPDEVVALGAAVQAGVLAGEV SDIVLLDVTPLSLGLETLGGVMTKLIPRNTTLPTSKSEVFSTAADGQTSVEINVLQGERE FARDNKSLGTFRLDGIPPAPRGVPQIEVKFDIDANGILSVTATDKGTSKKQDIRITGAST LDKGDVERMVKEAEKFAGEDKKRRESVETKNQAETMVYQTEKQLKEFEGKVPADIKAKVE AKLGELKAALPADDAEATKAAMNALQQEVMAMGQAMYSQAGAAPGGAPGAEPGAGAGAGG APGGKKDDDVIDAEFTDKK
Create BLAST database in a folder with the same name as the database. As an example here, the database would be the proteome of Chlamydomonas.
makeblastdb -in chlamydomonas.fa -dbtype prot -out chlamydomonas
Run BLASTp from the database folder
(Note: adjust the parameters to your needs; i.e. evalue & max_target_seqs)
(Note II: there are different ways to run blast locally. See BLASTall, BLASTn, etc; the parameters are not the same as in BLASTp)
blastp -query ../secuencias_query.fasta -db chlamydomonas -out ../resultados_blastp.txt -evalue 0.05 -outfmt "6 std qcovs"
BLASTp output by column. Information of BLAST terms can be found in the glossary.