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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.
This page is a subsection of the list of sequence alignment software. Multiple alignment visualization tools typically serve four purposes: Aid general understanding of large-scale DNA or protein alignments; Visualize alignments for figures and publication; Manually edit and curate automatically generated alignments; Analysis in depth
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.
Proteome Analyst (PA) is a freely available web server and online toolkit for predicting protein subcellular localization, or where a protein resides in a cell. [1] [2] In the field of proteomics, accurately predicting a protein's subcellular localization, or where a specific protein is located inside a cell, is an important step in the large scale study of proteins.
The user provides a proteome in fasta format, and the system employs Psi-blast, Psipred and Modeller to predict protein function and subcellular localization. Proteome Analyst uses machine-learned classifiers to predict things such as GO molecular function.
UniProt Archive (UniParc) is a comprehensive and non-redundant database, which contains all the protein sequences from the main, publicly available protein sequence databases. [17] Proteins may exist in several different source databases, and in multiple copies in the same database.
The output is the predicted peptide sequences in the FASTA format, and a definition line that includes the query ID, the translation reading frame and the nucleotide positions where the coding region begins and ends. OrfPredictor facilitates the annotation of EST-derived sequences, particularly, for large-scale EST projects.
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.