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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. The format allows for sequence names and comments to precede the sequences.
The original FASTA program was designed for protein sequence similarity searching. Because of the exponentially expanding genetic information and the limited speed and memory of computers in the 1980s heuristic methods were introduced aligning a query sequence to entire data-bases.
Biological sequence formats are a collection of file formats that are used in the biomedical sciences. There are a number of these. There are a number of these. Most of these formats were developed for use in particular programmes and have subsequently been reused by other programmes.
BLASTp, or Protein BLAST, is used to compare protein sequences. You can input one or more protein sequences that you want to compare against a single protein sequence or a database of protein sequences. This is useful when you're trying to identify a protein by finding similar sequences in existing protein databases. [18]
A PWM has one row for each symbol of the alphabet (4 rows for nucleotides in DNA sequences or 20 rows for amino acids in protein sequences) and one column for each position in the pattern. In the first step in constructing a PWM, a basic position frequency matrix (PFM) is created by counting the occurrences of each nucleotide at each position.
Another possibility is to request the strict ClustalW output format with the option "-output=clustalw_aln". An important specificity of T-Coffee is its ability to combine different methods and different data types. In its latest version, T-Coffee can be used to combine protein sequences and structures, RNA sequences and structures.
Fast statistical alignment or FSA is a multiple sequence alignment program for aligning many proteins, RNAs, or long genomic DNA sequences.Along with MUSCLE and MAFFT, FSA is one of the few sequence alignment programs which can align datasets of hundreds or thousands of sequences.
Biopython can read and write to a number of common sequence formats, including FASTA, FASTQ, GenBank, Clustal, PHYLIP and NEXUS. When reading files, descriptive information in the file is used to populate the members of Biopython classes, such as SeqRecord. This allows records of one file format to be converted into others.