Flexible sequence similarity searching with the FASTA3 program package.

By William R. Pearson. Methods in molecular biology, 2000

649 citations recorded by the source corpus.

Subfields: Artificial Intelligence, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/34a24084853773ca7c52c81704bbc70ddf93247c

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Citations in the corpus

Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones (2004, positive): “We predicted ORFs in all 41,118 H-Inv cDNAs, as illustrated in Figure S1, based on the alignment of similarity searches by FASTY (Pearson 2000; Mackey et al. 2002) (ver.”
Distribution and drivers of ectomycorrhizal fungal communities across the North American Arctic (2012, methodology): “In order to identify the OTUs, we compared the ITS sequences to a curated database derived from GenBank sequences hosted on the Fungal Metagenomics website (http://biotech.inbre. alaska.edu/fungal-metagenomics/), using the FASTA matching algorithm (Pearson 2000).”
MSAViewer: interactive JavaScript visualization of multiple sequence alignments (2016, positive): “The MSAViewer loads MSA data in FASTA (Pearson, 2000) or CLUSTAL (Larkin et al. , 2007) formats from a user’s local computer or a web server.”
Versatile and open software for comparing large genomes (2004, methodology): “This 'match and extend' step in the algorithm is essentially the same as that used by FASTA [29], BLAST [30], and many other sequence-alignment programs.”
Accelerated Profile HMM Searches (2011, methodology): “The heuristic approaches in BLAST and FASTA have the advantage of focusing subsequent slower computations on particular diagonals, whereas in HMMER’s current approach, we wastefully recalculate full sequence alignments at each step of the acceleration pipeline.”
BIOPEP-UWM Database of Bioactive Peptides: Current Opportunities (2019, methodology): “The FASTA format [94] is used to input a set of sequences.”
MIPS: analysis and annotation of proteins from whole genomes in 2005 (2005, methodology): “The similarity searches were carried out using the FASTA ( 13 ) package.”
Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. (2001, methodology): “It was made sure that no two proteins from different sets were more than 25 % identical in a Needleman-Wunsch alignment by the ALIGN program in the FASTA package (Pearson, 2000).”