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.

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Presentation transcript:

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 lhttp:// l

FASTA sequence format

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

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.TFASTXTFASTY FASTF/TFASTF Compares an ordered peptide mixtureFASTFTFASTF FASTS/TFASTS Compares set of short peptide fragments, as would be obtained from mass- spec.FASTSTFASTS

Output: Hit list

Alignment of query to a hit

Exercise Align two sequences by FASTA and SSEARCH fastahttp://gel.ym.edu.tw/~wxluo/lec5/eco_hslv. fasta astahttp://gel.ym.edu.tw/~wxluo/lec5/vch_hslv.f asta

Useful links

FASTA method

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: 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: html

Exercise Blast two sequences against sequence database fastahttp://gel.ym.edu.tw/~wxluo/lec5/eco_hslv. fasta astahttp://gel.ym.edu.tw/~wxluo/lec5/vch_hslv.f asta