A Greedy Algorithm for Aligning DNA Sequences

By Zheng Zhang, Scott Schwartz, L. Wagner, Webb Miller. J. Comput. Biol., 2000

5,462 citations recorded by the source corpus.

Subfields: Artificial Intelligence, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/070eb63031af260d840534b33fd8385b7152fda6

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Artificial Intelligence

1. Heng Li
2. Richard Durbin
3. Steven L. Salzberg
4. Robert A. Edwards
5. Florian P. Breitwieser
6. Mark J. P. Chaisson
7. Daehwan Kim
8. Glenn Tesler

In Molecular Biology

1. Steven L. Salzberg
2. Heng Li
3. Stephen H. Bryant
4. Richard Durbin
5. Florian P. Breitwieser
6. Thomas L. Madden
7. Mark J. P. Chaisson
8. Adam M. Phillippy

Citations in the corpus

• Endophytes as potential pathogens of the baobab species Adansonia gregorii: a focus on the Botryosphaeriaceae (2011, methodology): “Identities of non-botryosphaeriaceous isolates were determined by sequence similarity (Zhang et al. 2000) from Blast searches in GenBank (http://blast.ncbi.nlm.nih.gov/blast.cgi).”
• Field and Laboratory Methods for DNA Studies on Deep-sea Isopod Crustaceans (2014, background): “As a result, using the megablast search (Altschul et al. 1990; Zhang et al. 2000) in the context of contamination checking, the most frequent results comprise insects.”
• Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory (2012, methodology): “For example, reads produced by Sanger sequencing that are highly accurate and nearly 1000 bases long are successfully mapped using hash-based methods such as MEGABLAST [2], cross match (Green P.”
• CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers (2015, methodology): “Another important difference is that the method presented in [30] relies on M EGABLAST [31] to perform the classification, which is several orders of magnitude slower than K RAKEN [11].”
• Foliar endophytic fungi from Hevea brasiliensis and their antagonism on Microcyclus ulei (2011, methodology): “For the identification of fungal isolates, percentages of sequence identity and coverage were determined by comparative similarity analysis with available sequences in GenBank (http://www.ncbi.nlm.nih.gov) using Blastn (Zhang et al. 2000).”
• Centrifuge: rapid and sensitive classification of metagenomic sequences (2016, methodology): “The run-time memory footprint of MegaBLAST is small (Table 2) because it does not read the entire database into memory, in contrast to Kraken and Centrifuge.”
• Database resources of the National Center for Biotechnology Information (2011, background): “The default search program for the NCBI Genomic BLAST pages is MegaBLAST (15), a faster version of standard nucleotide BLAST designed to find alignments between nearly identical sequences, typically from the same species.”
• BLAST: at the core of a powerful and diverse set of sequence analysis tools (2004, background): “The fastest program is megaBLAST, which defaults to a large word-size (an exact match of 28 bases is required to initiate an extension) and a greedy gapped extension algorithm ( 4 ) that has no gap existence cost but merely a gap extension cost, making it ideal for comparing similar sequences (e.g.”
• Paralytic shellfish toxins or spirolides? The role of environmental and genetic factors in toxin production of the Alexandrium ostenfeldii complex (2013, neutral): “26+ (Zhang et al., 2000).”
• Database resources of the National Center for Biotechnology Information: update (2004, methodology): “Discontiguous MegaBLAST is far more rapid than a translated search such as blastx, yet maintains a competitive degree of sensitivity when comparing coding regions.”
• Phosphate-solubilizing microorganisms associated with the rhizosphere of oil palm (Elaeis guineensis Jacq.) in Colombia (2014, methodology): “8S, and ITS2 for fungi, and 16S gene for bacteria) were used s query sequences to search for similar sequences available in he NCBI database (Genomic Reference Sequences: reseq genomic) sing the BLAST algorithm (Zhang et al., 2000).”
• Database resources of the National Center for Biotechnology Information (2009, background): “For rapid cross-species nucleotide queries, NCBI offers Discontiguous MegaBLAST, which uses a noncontiguous word match (16) as the nucleus for its alignments.”