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The current FASTA package contains programs for protein:protein, DNA:DNA, protein:translated DNA (with frameshifts), and ordered or unordered peptide searches. Recent versions of the FASTA package include special translated search algorithms that correctly handle frameshift errors (which six-frame-translated searches do not handle very well ...
In bioinformatics and biochemistry, the FASTA format is a text-based format for representing either nucleotide sequences or amino acid (protein) sequences, in which nucleotides or amino acids are represented using single-letter codes.
FASTA: Local search with fast k-tuple heuristic, slower but more sensitive than BLAST: Both: GGSEARCH, GLSEARCH Global:Global (GG), Global:Local (GL) alignment with statistics: Protein: Genome Magician Software for ultra fast local DNA sequence motif search and pairwise alignment for NGS data (FASTA, FASTQ). DNA: Hepperle D (www.sequentix.de ...
FASTA provides a similar set of programs for comparing proteins to protein and DNA databases, DNA to DNA and protein databases, and includes additional programs for working with unordered short peptides and DNA sequences. In addition, the FASTA package provides SSEARCH, a vectorized implementation of the rigorous Smith-Waterman algorithm. FASTA ...
In the FASTA method, the user defines a value k to use as the word length with which to search the database. The method is slower but more sensitive at lower values of k, which are also preferred for searches involving a very short query sequence. The BLAST family of search methods provides a number of algorithms optimized for particular types ...
Align DNA, RNA, protein, or DNA + protein sequences via a variety of pairwise and multiple sequence alignment algorithms, generate phylogenetic trees to predict evolutionary relationships, explore sequence tracks to view GC content, gap fraction, sequence logos, translation ABI, DNA Multi-Seq, FASTA, GCG Pileup, GenBank, Phred
YASS (Yet Another Similarity Searcher) [1] [2] is a free software, [3] pairwise sequence alignment software for nucleotide sequences, that is, it can search for similarities between DNA or RNA sequences. YASS accepts nucleotide sequences in either plain text or the FASTA format and the output format includes the BLAST tabular output.
FASTQ format is a text-based format for storing both a biological sequence (usually nucleotide sequence) and its corresponding quality scores.Both the sequence letter and quality score are each encoded with a single ASCII character for brevity.
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