Difference between revisions of "Resource software"
From Bioinformatikpedia
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== Mapping sequence identifiers == |
== Mapping sequence identifiers == |
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| + | === Protein sequence databases === |
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| − | Here are a number of suggestions how to map identifiers between [http://www.ncbi.nlm.nih.gov/RefSeq/key.html#accessions Refseq] and other identifiers contained in NR and [http://www.uniprot.org/help/mapping Uniprot]. |
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| + | Here are a number of suggestions how to map identifiers between [http://www.ncbi.nlm.nih.gov/RefSeq/key.html#accessions Refseq] and other identifiers contained in NR and [http://www.uniprot.org/help/mapping 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. |
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* Use the mapping tool at [http://www.uniprot.org/help/mapping Uniprot] (see also [http://www.uniprot.org/faq/44 Uniprot FAQ]). Be careful to separate out the different types of identifiers (Genbank, Refseq, ...). |
* Use the mapping tool at [http://www.uniprot.org/help/mapping Uniprot] (see also [http://www.uniprot.org/faq/44 Uniprot FAQ]). Be careful to separate out the different types of identifiers (Genbank, Refseq, ...). |
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* Use [http://mips.gsf.de/genre/proj/cronos/index.html CRONOS] on the web or as a web service. |
* Use [http://mips.gsf.de/genre/proj/cronos/index.html CRONOS] on the web or as a web service. |
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Revision as of 16:06, 24 May 2011
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.
