05_BLAST

By Yan Li

PhD in Bioinformatics, University of Liverpool

BLAST

  • Basic Local Alignment Search Tool
  • Compare a query sequence against a database
  • Sequence alignment: local & pairwise

Homology

  • Similarity
  • Homology: diverged from a common ancestor
  • Orthologues: proteins that do the same function in different species
  • Paralogues: proteins that perform different, but related functions within one organism

Orthologues vs Paralogues

homology

Blast program

blast

DNA potentially encodes six proteins

DNA_6_proteins

BLAST program

blast-program

BLAST hit list

blast_hit_list

BLAST alignment

blast_alignment

e-value

  • Number of matches with this score one can expect to find by chance in a database of size N
  • Closer to 0, the better the alignment

blastn vs blastp

  • Faster and more accurate to BLAST proteins rather than nucleotides.
  • If you know the reading frame in your sequence – TRANSLATE it and then BLAST

Online BLAST workshop

NCBI (National Center for Biotechnology Information) server:

https://www.ncbi.nlm.nih.gov/BLAST

local BLAST software

conda install -c bioconda blast
makeblastdb -in sopd_gene.fasta -dbtype nucl -out sopD
blastn -query salmonella_typhimurium_lt2.fasta -db sopD -out sopD_lt2.txt -outfmt 1
  • Read the help document
  • Make notes of all your operations