FASTA protocols

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FASTA specifications

Information


Unique identifier OMICS_00994
Name FASTA
Alternative names FASTA2, FASTA3
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/FASTA

Maintainer


  • person_outline William Pearson <>

Publications for FASTA

FASTA in pipelines

 (7)
2018
PMCID: 5868767
PMID: 29579047
DOI: 10.1371/journal.pone.0192851

[…] environment for the display of phylogenetic trees, a program for creating multiple sequence alignments, program for clustering protein sequences based on bit scores derived from blastp, ssearch36, fasta36 or ublast, a program for building phylogenetic trees, a suite of programs for phylogenetic analysis, program for constructing protein trees using blast bit scores rather than multiple […]

2017
PMCID: 5595812
PMID: 28900103
DOI: 10.1038/s41598-017-10902-0

[…] the bigdye® terminator v3.1 cycle sequencing kit (applied biosystems) by the australian equine genetics research centre., the prevalence and sequence conservation of yeej was examined using the fasta36 software package to probe 96 complete e. coli genomes on the national centre for biotechnology information (ncbi) database (figure ). the prevalence of genes was determined using a cut-off […]

2016
PMCID: 5066493
PMID: 27619233
DOI: 10.1093/jxb/erw338

[…] numbers gse74384 and gse74132, respectively., the conserved mirnas were identified by comparing the srna reads with the known plant mirnas registered in mirbase (http://www.mirbase.org/) () using fasta36 (http://faculty.virginia.edu/wrpearson/fasta/fasta36/), allowing three mismatches. the novel mirnas were identified from the unmatched reads. the putative mirna precursors were identified […]

2011
PMCID: 3027613
PMID: 21297863
DOI: 10.1371/journal.pone.0014519

[…] sequence from methanoculleus bourgensis (genbank accession ay196674) was used as an assembly template. the pyrosequencing reads were aligned to the reference sequence using ‘align0’ from the fasta3 package and then clustered into several groups based on their snp (single nucleotide polymorphism) content. afterwards, each of the resulting groups of reads was separately assembled […]

2011
PMCID: 3068122
PMID: 21406087
DOI: 10.1186/1471-213X-11-19

[…] and information in ncbi http://www.ncbi.nlm.nih.gov, blast http://www.ncbi.nlm.nih.gov/blast, flybase http://flybase.org/, clustalw http://www.ebi.ac.uk/clustalw and fasta http://www.ebi.ac.uk/tools/fasta33/index.htm databases., ik performed the experiments. mfr supervised the molecular biology experiments. ls conceived and supervised the study, and wrote the manuscript. all authors contributed […]


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FASTA in publications

 (85)
PMCID: 5868767
PMID: 29579047
DOI: 10.1371/journal.pone.0192851

[…] as implemented in the r package (https://www.r-project.org/) on a distance matrix calculated from bit scores produced from local protein alignments within the superfamily performed with blastp [], fasta36 [], ssearch [], or ublast []. clusters were produced using the ward agglomerative method. superfamilytree uses tens of thousands of blast bit scores to derive 100 sampled trees [–]. […]

PMCID: 5704145
PMID: 29156611
DOI: 10.3390/foods6110101

[…] inc., foster city, ca, usa). the sequence data was collected using the abi 610 software (applied biosystems inc.) and analyzed with fasta programming (european bioinformatics, http://www2.ebi.ac.uk/fasta3/) , in this experiment, extracts of porcine hemoglobin were probed with mab 24c12-e7 using both ielisa and western blot. porcine blood was run alongside as the control for comparison. […]

PMCID: 5705957
PMID: 29072602
DOI: 10.3390/toxins9110342

[…] and sp6 promoters. the dna sequence data were analyzed and translated into the amino acid sequence using mega 6 software []. protein sequence homology in the swiss-prot database was searched using fasta3 [] and sequence alignments were generated with clustal w 2.1. the theoretical isoelectric point was calculated with expasy []., for the first dimension, 30 µg of bacol pla2 was applied to a 7 […]

PMCID: 5813221
PMID: 28921896
DOI: 10.1002/mnfr.201700297

[…] allergen list and sequence database that is updated each year. we used the aol as the primary tool in searching for matches to allergenic sequences. three comparison methods were used: an overall fasta3 full‐length search (using e scores of 10 and 1.0), a sliding 80 aa window fasta search (e score of 10, identity > 35%), and an exact word search tool looking for eight aa exact matches. […]

PMCID: 5645381
PMID: 29042670
DOI: 10.1038/s41598-017-13876-1

[…] est clones based on their characterization study. sequenced: a clone was sequenced and filed in this study; identified: a clone matches a sequence at the amino acid level in the public database of fasta3; annotated: a clone is similar in sequence to a protein or dna whose annotation is available in the database; non-redundant: an annotated clone that appeared only once in est library; […]


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FASTA institution(s)
Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA

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