FASTA program

Similarity search can be performed with the FASTA program, though BLAST is easier to use. Both FASTA and BLAST homology searches are also available at EBI, PIR and DDBJ. The small P values indicate homologous sequences. 

To improve this unsatisfying situation, many bioinformatics sites construct nonredundant databases from a number of component databases, or they use external nonredundant databases, e.g., OWL (Bleasby et al., 1994). Both strategies considerably improve the situation for the end user, but they require the time- and resource-consuming maintenance of multiple databases or the acceptance of a certain time lag between creation of an entry and its appearance in the nonredundant database. Furthermore, both strategies lead to a loss of information in the individual entry owing to the diversity of database formats. Whereas OWL preserves most information of an entry and some of its structure, the NRDB program requires a conversion of the component databases to FASTA format, which contains only one description line per entry. 

SPTR is distributed in three files sprot.dat.Z, trembl.dat.Z, and trembl new.dat.Z. These files are, as indicated by their Z extension, Unix compress format files, which, when decompressed, produce ASCII files in SWISS-PROT format. Three others files are also available (sprot.fas.Z, trembl.fas.Z, and trembl new.fas.Z), which are compressed fasta format sequence files that are useful for building the databases used by FASTA, BLAST, and other sequence similarity search programs. These files should not be used for other purposes, because all annotation is lost when using this format. The SPTR files are stored in the directory /pub/databases/sp tr nrdb on the EBI FTP server (ftp.ebi.ac.uk) and in the directory /databases/sp tr nrdb on the ExPASyFTP server (ftp. expasy.ch). 

Sequence similarity search tools Alignments of the query sequence with databases produce sequence similarity. The BLAST series of programs has variants that will translate DNA databases, translate the input sequence, or both. FASTA provides a similar suite of programs. 

Database search programs like FASTA [18] or BLAST [19] have been optimised to detect evolutionary relationships between proteins, and are readily adequate for template recognition and (multiple) sequence alignment in cases where the sequence identity is over 25-30% [20], The general procedure is to assume next that the backbone of the model is identical to the one of the template structure and add the side chains onto it [21], although some difficulties may arise with insertions, deletions and local low similarity. 

Several implementations of this procedure are available, most prominently the SSEARCH program from the FASTA package [53], There exist implementations of the Smith-Waterman algorithm that are tuned for speed like one using special processor instructions [54] and, among others, one by Barton [55], Depending on implementation, computer, and database size, a search with such a program will take on the order of one minute. 

Like FASTA, BLAST has also been adapted to connect good diagonals and report local alignments with gaps. BLAST converts the database file into its own format to allow for faster reading. This makes it somewhat unwieldy to use in a local installation unless someone takes care of the installation. FASTA, on the other hand, is slower but easier to use. There exist excellent web servers that offer these programs, in particular at the National Center for Biotechnology Information (NCBI [59]) and at the European Bioinformatics Institute (EBI [60]) where BLAST or FASTA can be used on up-to-date DNA and protein databases. 

In additional to the human-readable DIALIGN alignment format, the program can return the output alignment in FASTA or MSF format. 

Fig. 2. Each sequence can be pasted in, in FASTA format, uploaded as a FASTA file, or entered as an accession number along with the available annotation (A). Alternatively, sequences can be fetched from the UCSC Genome Browser individually using the Upload function (A), or in groups (Batch Upload System) Browser (B). Once sequences have been uploaded, the program acknowledges the receipt (C).

---