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Comparing Compressed Sequences for Faster Nucleotide BLAST Searches
July-September 2007 (vol. 4 no. 3)
pp. 349-364
ASCII Text
x 
 
Michael Cameron, Hugh Williams, "Comparing Compressed Sequences for Faster Nucleotide BLAST Searches," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 4, no. 3, pp. 349-364, July-September, 2007.
 
 
BibTex
x
 
@article{ 10.1109/TCBB.2007.1029,
author = {Michael Cameron and Hugh Williams},
title = {Comparing Compressed Sequences for Faster Nucleotide BLAST Searches},
journal ={IEEE/ACM Transactions on Computational Biology and Bioinformatics},
volume = {4},
number = {3},
issn = {1545-5963},
year = {2007},
pages = {349-364},
doi = {http://doi.ieeecomputersociety.org/10.1109/TCBB.2007.1029},
publisher = {IEEE Computer Society},
address = {Los Alamitos, CA, USA},
}
 
 
RefWorks Procite/RefMan/Endnote
x 
 
TY - JOUR
JO - IEEE/ACM Transactions on Computational Biology and Bioinformatics
TI - Comparing Compressed Sequences for Faster Nucleotide BLAST Searches
IS - 3
SN - 1545-5963
SP349
EP364
EPD - 349-364
A1 - Michael Cameron,
A1 - Hugh Williams,
PY - 2007
KW - Homology search
KW - BLAST
KW - sequence alignment
KW - compression
KW - Four Russians algorithm
VL - 4
JA - IEEE/ACM Transactions on Computational Biology and Bioinformatics
ER -
 
Molecular biologists, geneticists, and other life scientists use the BLAST homology search package as their first step for discovery of information about unknown or poorly annotated genomic sequences. There are two main variants of BLAST: BLASTP for searching protein collections and BLASTN for nucleotide collections. Surprisingly, BLASTN has had very little attention; for example, the algorithms it uses do not follow those described in the 1997 BLAST paper [1] and no exact description has been published. It is important that BLASTN is state-of-the-art: Nucleotide collections such as GenBank dwarf the protein collections in size, they double in size almost yearly, and they take many minutes to search on modern general purpose workstations. This paper proposes significant improvements to the BLASTN algorithms. Each of our schemes is based on compressed bytepacked formats that allow queries and collection sequences to be compared four bases at a time, permitting very fast query evaluation using lookup tables and numeric comparisons. Our most significant innovations are two new, fast gapped alignment schemes that allow accurate sequence alignment without decompression of the collection sequences. Overall, our innovations more than double the speed of BLASTN with no effect on accuracy and have been integrated into our new version of BLAST that is freely available for download from http://www.fsa-blast.org/.

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Index Terms:
Homology search, BLAST, sequence alignment, compression, Four Russians algorithm
Citation:
Michael Cameron, Hugh Williams, "Comparing Compressed Sequences for Faster Nucleotide BLAST Searches," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 4, no. 3, pp. 349-364, July-Sept. 2007, doi:10.1109/TCBB.2007.1029
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