BLAST 2 Sequences, a new tool for comparing protein and nucleotide sequences
Abstract
'BLAST 2 Sequences', a new BLAST-based tool for aligning two protein or nucleotide sequences, is described. While the standard BLAST program is widely used to search for homologous sequences in nucleotide and protein databases, one often needs to compare only two sequences that are already known to be homologous, coming from related species or, e.g. different isolates of the same virus. In such cases searching the entire database would be unnecessarily time-consuming. 'BLAST 2 Sequences' utilizes the BLAST algorithm for pairwise DNA-DNA or protein-protein sequence comparison. A World Wide Web version of the program can be used interactively at the NCBI WWW site (http://www.ncbi.nlm.nih.gov/gorf/bl2.++ +html). The resulting alignments are presented in both graphical and text form. The variants of the program for PC (Windows), Mac and several UNIX-based platforms can be downloaded from the NCBI FTP site (ftp://ncbi.nlm.nih.gov).
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BLAST is a widely-used algorithm for comparing an inquiry sequence against a database or reference sequence.
“The aasic local alignment search tool (BLAST) is a widely-used algorithm for comparing an inquiry sequence against a database or reference sequence [34].”
From Whole-Genome Alignment: Methods, Challenges, and Future Directions (2024) · cites this paper as [34]
BLAST employs hashing to rapidly find regions of local similarity, facilitating analyses from gene identification to comparative genomics.
“BLAST employs hashing to rapidly find regions of local similarity, facilitating a broad range of analyses from gene identification to comparative genomics;”
From Whole-Genome Alignment: Methods, Challenges, and Future Directions (2024) · cites this paper as [34]
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- Authors
- Tatusova, T. A., & Madden, T. L.
- Affiliations
- National Institutes of Health (US)
- Corresponding author
- Tatusova, Tatiana A
- ORCID
- Madden, Thomas L
- Venue
- FEMS Microbiology Letters
- Publisher
- Oxford University Press (OUP)
- Published
- 1999-05
- Volume
- 174
- Issue
- 2
- Pages
- 247-250
- ISSN
- 0378-1097 (ISSN-L)
- 1574-6968
- OpenAlex
- W2072603644
- Cited by
- 1,789
- References
- 5
- Citations by year
- 2026: 10 · 2025: 6 · 2024: 18 · 2023: 11 · 2022: 18 · 2021: 21 · 2020: 16 · 2019: 25 · 2018: 40 · 2017: 32 · 2016: 39 · 2015: 40 · 2014: 35 · 2013: 38 · 2012: 48
- FWCI
- 25.95
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- FEMS Microbiology Letters (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fractal and DNA sequence analysis
- Physical Sciences › Computer Science › Artificial Intelligence › Algorithms and Data Compression
- Keywords
- pairwise sequence alignment, homologous sequences, NCBI BLAST
- MeSH terms
- Algorithms, Amino Acid Sequence, Base Sequence, Software, Sequence Alignment
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