By Brian Golding and Dick Morton
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Additional resources for Brian sequence analysis
Both the GenBank and EMBL formats are highly stylized and strictly controlled to conform to consistent standards. 1, DNAStrider, Fitch, GCG, GDE, HENNIG86, IG/Stanford, MSF, NBRF, NEXUS. PIR/CODATA, Pearson/Fasta, Phylip - Interleaved, Phylip - Sequential, and Plain/Raw, I will not present all here but rather just a smattering. Most formats will ignore case and this can therefore often be used to add information about the sequences. While the GenBank and EMBL formats can contain the character ‘-’ (used to line up homologous sites among multiple sequences), they generally do not contian these characters and these formats were not intended to convey the kind of information that includes homologous sites between multiple sequences.
1 FASTA To search through the whole genetic sequence database can take a great deal of time due to its enormous size. If some operation must be performed on each sequence in turn then this can take even longer. One such example is to look throughout the whole database for homologous or similar sequences. To do this, special programs have been developed to speed the search. R. J. Lipman (1988, PNAS 85:2444-2448). It is possible to run this program on remote machines. The obvious choice for such a remote machine would be one that has access to the latest sequence information.
For example, release 38 of SWISS- PROT contains 80,000 annotated entries containing a total of 29,085,965 amino acid residues. There are more than 232 entries having proteins larger than 2500 residues including one that is a massive protein of 5255 amino acids. The entries in this database are similar to the nucleotide databases of EMBL. Two examples are shown below. Example Entry #5: SWISS-PROT - ACYO HUMAN ID AC DT DT DT DE DE DE OS OC OC RN RP RX RA ACYO_HUMAN STANDARD; PRT; 98 AA. P07311; 01-APR-1988 (REL.
Brian sequence analysis by Brian Golding and Dick Morton