Fasta and blast
Download
1 / 28

FASTA and BLAST - PowerPoint PPT Presentation


  • 449 Views
  • Uploaded on

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.

loader
I am the owner, or an agent authorized to act on behalf of the owner, of the copyrighted work described.
capcha
Download Presentation

PowerPoint Slideshow about 'FASTA and BLAST' - Jeffrey


An Image/Link below is provided (as is) to download presentation

Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author.While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server.


- - - - - - - - - - - - - - - - - - - - - - - - - - E N D - - - - - - - - - - - - - - - - - - - - - - - - - -
Presentation Transcript

Fasta introduction l.jpg
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 l.jpg
fasta

  • http://fasta.bioch.virginia.edu/

  • http://www.ebi.ac.uk/fasta33/

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



Slide5 l.jpg

  • 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.


Slide6 l.jpg

  • 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.





Exercise l.jpg
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 l.jpg
Useful links

  • http://www.ebi.ac.uk/2can/home.html

  • http://fasta.genome.jp/

  • http://blast.genome.jp/

  • http://www.ebi.ac.uk/fasta33/



Blast l.jpg
BLAST

  • http://www.ncbi.nih.gov/BLAST



Running standalone ncbi blast l.jpg
Running standalone NCBI BLAST

  • formatdb –i input.fasta –o T –p T

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


References l.jpg
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


Exercise28 l.jpg
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/