Resource software

Here, we collect descriptions of the software used in the practical. This can be software used in online portals or software installed locally on your own computers or the lab resources. In each case, please describe how to access the software and where to find manuals. Also use this site to collect scripts or HOW_TOs that could be useful for others.

Mapping sequence identifiers

Protein sequence databases

Here are a number of suggestions how to map identifiers between Refseq and other identifiers contained in NR and Uniprot. -- Be careful: Refseq identifiers have version numbers (.n). Not all mapping tools take these into account or are able to cope with the attached version number. So if you use a mapping tool, look for the documentation of the input and output.

• Use the mapping tool at Uniprot (see also Uniprot FAQ). Be careful to separate out the different types of identifiers (Genbank, Refseq, ...).
• Use CRONOS on the web or as a web service.
• Use SRS (sequence retrieval system) on the web (e.g. at EMBL, EBI, or any other installation) to do a query for a list of sequences. You can also do this programatically, but then you have to have access to and learn how to use the web services.

Changing Blast output

By default, Blast lists 500 search hits and 250 alignment details. This can be changed (see Blast manual for details):

• You can use a custom output format to get a table with "-m 8" (see "-help" or this hint on how to parse Blast output).
• You can use "-b" to set the number of alignments to be shown, "-b 20000" is the maximum.