FASTA and BLAST

FASTA: Introduction

• FASTA  (pronounced FAST-Aye) stands for FAST-All, reflecting the fact that it can be used for a fast protein comparison or a fast nucleotide comparison

• This is achieved by performing optimized searches for local alignments using a substitution matrix.

• The high speed of this program is achieved by using the observed pattern of word hits to identify potential matches before attempting the more time consuming optimized search.

fasta

• http://fasta.bioch.virginia.edu/

• http://www.ebi.ac.uk/fasta33/

• http://www.ebi.ac.uk/fasta33/genomes.html

FASTA sequence format

• FASTA Compares a protein sequence to another protein sequence or to a protein database

• FASTX/FASTY Compares a DNA sequence to a protein sequence database, translating the DNA sequence in three forward (or reverse) frames and allowing frameshifts.

• TFASTX/TFASTY Compares a protein sequence to a DNA sequence or DNA sequence library. The DNA sequence is translated in three forward and three reverse frames, and the protein query sequence is compared to each of the six derived protein sequences.

• FASTF/TFASTF Compares an ordered peptide mixture

• FASTS/TFASTS Compares set of short peptide fragments, as would be obtained from mass-spec.

FASTA@EBI

Output: Hit list

Alignment of query to a hit

Exercise

• Align two sequences by FASTA and SSEARCH

• http://gel.ym.edu.tw/~wxluo/lec5/eco_hslv.fasta

• http://gel.ym.edu.tw/~wxluo/lec5/vch_hslv.fasta

• http://www.ebi.ac.uk/fasta33/

Useful links

• http://www.ebi.ac.uk/2can/home.html

• http://fasta.genome.jp/

• http://blast.genome.jp/

• http://www.ebi.ac.uk/fasta33/

FASTA method

BLAST

• http://www.ncbi.nih.gov/BLAST

BLAST programs

Running standalone NCBI BLAST

• formatdb –i input.fasta –o T –p T

• blastall –p blastp –d db –i query.fasta –o blast.result

References

• Altschul, S.F., Gish, W., Miller, W., Myers, E.W. & Lipman, D.J. (1990) "Basic local alignment search tool." J. Mol. Biol. 215:403-410.

• Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D.J. (1997) "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs." Nucleic Acids Res. 25:3389-3402

• http://www.ncbi.nlm.nih.gov/blast/producttable.shtml

Exercise

• Blast two sequences against sequence database

• http://gel.ym.edu.tw/~wxluo/lec5/eco_hslv.fasta

• http://gel.ym.edu.tw/~wxluo/lec5/vch_hslv.fasta

• http://www.ebi.ac.uk/fasta33/

• http://bioinfo.nchc.org.tw/