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Running BLASTp locally

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

Locally with the command line

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.

  1. query
  2. hit
  3. identity
  4. alignment length
  5. #mismatch
  6. #gaps
  7. start query
  8. end query
  9. hit start
  10. hit end
  11. e-value → we want this close to zero
  12. bit score
  13. Coverage

Noted issues

  • In BLASTn, sequences with a repeated pattern of nucleotides may not always be found through BLAST due to the low complexity filter.
  • Keep in mind the limitations of BLAST.