FASTA and BLAST

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FASTA and BLAST
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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.

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fasta

• http//fasta.bioch.virginia.edu/
• http//www.ebi.ac.uk/fasta33/
• http//www.ebi.ac.uk/fasta33/genomes.html

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FASTA sequence format
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• 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.

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• 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.

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FASTA_at_EBI
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Output Hit list
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Alignment of query to a hit
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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/

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Useful links

• http//www.ebi.ac.uk/2can/home.html
• http//fasta.genome.jp/
• http//blast.genome.jp/
• http//www.ebi.ac.uk/fasta33/

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FASTA method
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BLAST

• http//www.ncbi.nih.gov/BLAST

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BLAST programs
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Running standalone NCBI BLAST

• formatdb i input.fasta o T p T
• blastall p blastp d db i query.fasta o
  blast.result

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References

• Altschul, S.F., Gish, W., Miller, W., Myers, E.W.
  Lipman, D.J. (1990) "Basic local alignment
  search tool." J. Mol. Biol. 215403-410.
• 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. 253389-3402
• http//www.ncbi.nlm.nih.gov/blast/producttable.sht
  ml

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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/