GWFASTA is a webserver intended for the objective of aiding researchers in their quest for sequence similarity searching and analysis on a genome wide scale.
Sequence alignments provide a powerful way to compare novel sequences with previously characterized genes. Both functional and evolutionary information can be inferred from well designed queries and alignments. Pairs of protein and DNA sequences can be rapidly aligned using FASTA. It looks for matching sequence patterns or words, called k-tuples, and then attempts to build a local alignment based on these word matches. This is unlike a much slower but more sensitive Smith-Waterman algorithm developed for similarity searching before FASTA. FASTA is comparable in reliability and in algorithm to BLAST but is more sensitive to searches for protein sequence families and should be peferred more for DNA searches instead of BLAST.
FASTA compares an input DNA or protein sequence to all sequences in a target sequence database, and then reports the best matched sequences and local alignments of these matched sequence with the input sequence. The input sequence and database are usually in FASTA format.
If you use GWFASTA please cite the following paper:
Issac, B. and Raghava, G. P. S.(2002) GWFASTA: A server for FASTA search in Eukaryotic and Microbial genomes. BioTechniques 33(3):548-556.
| SEARCH AGAINST | |
| Standard Protein Databases | Standard Nucleotide Databases |
| Prokaryotic Proteome Databases | Prokaryotic Genomic Databases |
| Eukaryotic Proteome Databases | Eukaryotic Genomic Databases |
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