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Protocols

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 citations

 (99)
library_books

Bioinformatic characterization of the Anoctamin Superfamily of Ca2+ activated ion channels and lipid scramblases

2018
PLoS One
PMCID: 5868767
PMID: 29579047
DOI: 10.1371/journal.pone.0192851

[…] ng 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 [–]. These tree […]

library_books

Immunodetection of Porcine Red Blood Cell Containing Food Ingredients Using a Porcine Hemoglobin Specific Monoclonal Antibody

2017
PMCID: 5704145
PMID: 29156611
DOI: 10.3390/foods6110101

[…] s 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/) […]

library_books

Isolation and Functional Characterization of an Acidic Myotoxic Phospholipase A2 from Colombian Bothrops asper Venom

2017
Toxins
PMCID: 5705957
PMID: 29072602
DOI: 10.3390/toxins9110342

[…] T7 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 []. […]

library_books

Evaluating Potential Risks of Food Allergy and Toxicity of Soy Leghemoglobin Expressed in Pichia pastoris

2017
PMCID: 5813221
PMID: 28921896
DOI: 10.1002/mnfr.201700297

[…] Searches with the LegHb AA sequence against AOL v16 did not identify any significant alignment with an allergen. Full length alignments from FASTA3 searches with E scores <1.0 are shown in Table S4, Supporting Information. Only one type of protein, the globin (insect Hb) from Chironomus thummi thummi, aligned with <27% identity, which is b […]

library_books

From EST to novel spider silk gene identification for production of spidroin based biomaterials

2017
Sci Rep
PMCID: 5645381
PMID: 29042670
DOI: 10.1038/s41598-017-13876-1

[…] s, all EST sequences were submitted to Mail-Fasta via email ([email protected]) for sequence homology search. The search was against all the DNA entries in the EMBL database (http://www.ebi.ac.uk/Tools/fasta33/index.html, UniProt). The first 100 most homologous sequences were listed, and usually the best 10–30 sequence alignments were examined. The identification of a spider homologous cDNA clone wa […]

library_books

YeeJ is an inverse autotransporter from Escherichia coli that binds to peptidoglycan and promotes biofilm formation

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

[…] 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 of […]

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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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