BLAST (Basic Local Alignment Search Tool) finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance.

CyVerse UK provides the following BLAST applications:

  • Create BLAST db, to create a database to use in one of the BLAST comparison tool.
  • BLASTp for nucleotide sequences comparison.
  • BLATn for protein sequences comparison.

See the NCBI BLAST page for more details.

  • 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.
  • Gish, W. & States, D.J. (1993) “Identification of protein coding regions by database similarity search.” Nature Genet. 3:266-272.
  • Madden, T.L., Tatusov, R.L. & Zhang, J. (1996) “Applications of network BLAST server” Meth. Enzymol. 266:131-141.
  • 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.
  • Zhang Z., Schwartz S., Wagner L., & Miller W. (2000), “A greedy algorithm for aligning DNA sequences” J Comput Biol 2000; 7(1-2):203-14.
  • Zhang, J. & Madden, T.L. (1997) “PowerBLAST: A new network BLAST application for interactive or automated sequence analysis and annotation.” Genome Res. 7:649-656.
  • Morgulis A., Coulouris G., Raytselis Y., Madden T.L., Agarwala R., & Schäffer A.A. (2008) “Database indexing for production MegaBLAST searches.” Bioinformatics 15:1757-1764.
  • Camacho C., Coulouris G., Avagyan V., Ma N., Papadopoulos J., Bealer K., & Madden T.L. (2008) “BLAST+: architecture and applications.” BMC Bioinformatics 10:421.
  • Boratyn GM, Schäffer AA, Agarwala R, Altschul SF, Lipman DJ, & Madden T.L. (2012) “Domain enhanced lookup time accelerated BLAST.” Biol Direct. 2012 Apr 17;7:12.
  • Altschul, S.F., Boguski, M.S., Gish, W. & Wootton, J.C. (1994) “Issues in searching molecular sequence databases.” Nature Genet. 6:119-129.
  • McGinnis S., & Madden T.L. (2004) “BLAST: at the core of a powerful and diverse set of sequence analysis tools.” Nucleic Acids Res. 32:W20-W25.
  • Ye J., McGinnis S, & Madden T.L. (2006) “BLAST: improvements for better sequence analysis.” Nucleic Acids Res. 34:W6-W9.
  • Johnson M, Zaretskaya I, Raytselis Y, Merezhuk Y, McGinnis S, & Madden T.L. (2008) “NCBI BLAST: a better web interface” Nucleic Acids Res. 36:W5-W9.
  • Boratyn GM, Camacho C, Cooper PS, Coulouris G, Fong A, Ma N, Madden TL, Matten WT, McGinnis SD, Merezhuk Y, Raytselis Y, Sayers EW, Tao T, Ye J, & Zaretskaya I. (2013) “BLAST: a more efficient report with usability improvements.” Nucleic Acids Res. 41:W29-W33.
  • Wootton, J.C. & Federhen, S. (1996) “Analysis of compositionally biased regions in sequence databases.” Meth. Enzymol. 266:554-571.
  • Wootton, J.C. & Federhen, S. (1993) “Statistics of local complexity in amino acid sequences and sequence databases.” Comput. Chem. 17:149-163.
  • Hancock, J.M. & Armstrong, J.S. (1994) “SIMPLE34: an improved and enhanced implementation for VAX and Sun computers of the SIMPLE algorithm for analysis of clustered repetitive motifs in nucleotide sequences.” Comput. Appl. Biosci. 10:67-70.
  • Dayhoff, M.O., Schwartz, R.M. & Orcutt, B.C. (1978) “A model of evolutionary change in proteins.” In “Atlas of Protein Sequence and Structure, vol. 5, suppl. 3.” M.O. Dayhoff (ed.), pp. 345-352, Natl. Biomed. Res. Found., Washington, DC.
  • Schwartz, R.M. & Dayhoff, M.O. (1978) “Matrices for detecting distant relationships.” In “Atlas of Protein Sequence and Structure, vol. 5, suppl. 3.” M.O. Dayhoff (ed.), pp. 353-358, Natl. Biomed. Res. Found., Washington, DC.
  • Altschul, S.F. (1991) “Amino acid substitution matrices from an information theoretic perspective.” J. Mol. Biol. 219:555-565.
  • States, D.J., Gish, W., Altschul, S.F. (1991) “Improved sensitivity of nucleic acid database searches using application-specific scoring matrices.” Methods 3:66-70.
  • Henikoff, S. & Henikoff, J.G. (1992) “Amino acid substitution matrices from protein blocks.” Proc. Natl. Acad. Sci. USA 89:10915-10919.
  • Altschul, S.F. (1993) “A protein alignment scoring system sensitive at all evolutionary distances.” J. Mol. Evol. 36:290-300.
  • Altschul, S.F. & Gish, W. (1996) “Local alignment statistics.” Meth. Enzymol. 266:460-480.
  • Karlin, S. & Altschul, S.F. (1990) “Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes.” Proc. Natl. Acad. Sci. USA 87:2264-2268.
  • Karlin, S. & Altschul, S.F. (1993) “Applications and statistics for multiple high-scoring segments in molecular sequences.” Proc. Natl. Acad. Sci. USA 90:5873-5877.
  • Dembo, A., Karlin, S. & Zeitouni, O. (1994) “Limit distribution of maximal non-aligned two-sequence segmental score.” Ann. Prob. 22:2022-2039.
  • Altschul, S.F. (1997) “Evaluating the statistical significance of multiple distinct local alignments.” In “Theoretical and Computational Methods in Genome Research.” (S. Suhai, ed.), pp. 1-14, Plenum, New York.
  • Schaffer AA, Aravind L, Madden TL, Shavirin S, Spouge JL, Wolf YI, Koonin EV, Altschul SF. (2001) “Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements.” Nucleic Acids Res. 2001 Jul 15;29(14):2994-3005.
  • Park Y, Sheetlin S, Ma N, Madden TL, & Spouge JL. (2012) “New finite-size correction for local alignment score distributions.” BMC Res Notes. 2012 Jun 12;5:286.
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