Download e-book for kindle: Brian sequence analysis by Brian Golding and Dick Morton

By Brian Golding and Dick Morton

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Sample text

Gov with the following example format for your query. DATALIB gb TITLES MAXDOCS 30 BEGIN BOVPRL J02459 [ACC] The DATALIB must be gb or genbank (GenBank), gbu or gbupdate (only updates since the last release), gbonly (official release only), emb or embl (EMBL), emblu or emblupdate (only updates since the last release), emblonly (full release only), sp or swiss or swissprot (Swiss-Prot), spu or swissprotupdate (updates only), pir (PIR Elementary Sequence Analysis edited by Brian Golding and Dick Morton Sept 2000 33 database), omim (OMIM), vector (vector sequences), gp or genpept (translated GenBank), gpu or gpuupdate (updates only), kabatnuc (immunological nucleotide sequences), kabatpro (immunological protein sequences), and, though not stated in the official documentation, MEDLINE also works.

The take home message from all of this is to look at the data with a critical eye. The actual quantity and type of errors within the databases are not known - some researchers are very careful and can check their sequence data, for others a double check of the sequence data may not be possible. When doing your own research, assume that the sequence may contain some errors and take measures to prevent this from destroying your conclusions. 10 Sequence File Formats There are many formats that sequence data can be presented in.

An ‘offset’ of 36 means to insert 36 ‘-’ in front of the sequence in order to properly line it up with the other sequences. This format can also contain all the information that is present in a GenBank format but does so simply as a ‘comment’ enclosed in quotation marks and any information may appear within the comment field. As an example, I will use a proportion of the Mus pahari, Mus spicilegus and Gerbillus campestris APRT gene sequences. A GDE format for these sequences is 36 { name "MPU28721" type "DNA" longname Mus pahari sequence-ID "U28721" descrip "Mus pahari adenine phosphoribosyltransferase (APRT) gene, complete cds" creator "Fieldhouse,D.

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