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revision 1.4, Wed Aug 5 19:33:24 2009 UTC revision 1.5, Thu Aug 6 16:00:43 2009 UTC
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7    
8  The B<Sapling Server> is a web service that allows you to access data stored in  The B<Sapling Server> is a web service that allows you to access data stored in
9  the Sapling database, a large-scale MySQL database of genetic data. The Sapling  the Sapling database, a large-scale MySQL database of genetic data. The Sapling
10  database contains data on public genomes imported from L<RAST|http://rast.nmpdr.org>  database contains data on public genomes imported from I<RAST> (L<http://rast.nmpdr.org>)
11  and curated by the annotation team of the Fellowship for Interpretation of  and curated by the annotation team of the Fellowship for Interpretation of
12  Genomes.  Genomes.
13    
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176  Bacillus halodurans C-125 (I<272558.1>).  Bacillus halodurans C-125 (I<272558.1>).
177    
178  Frequently, however, you will have a list of gene IDs from some other  Frequently, however, you will have a list of gene IDs from some other
179  database (e.g. L<NCBI|http://www.ncbi.nlm.nih.gov>, L<UniProt|http://www.uniprot.org>)  database (e.g. I<NCBI> (L<http://www.ncbi.nlm.nih.gov>), I<UniProt> (L<http://www.uniprot.org>))
180  or in a community format such as Locus Tags or gene names. Most services that  or in a community format such as Locus Tags or gene names. Most services that
181  take gene IDs as input allow you to specify a C<source> option that indicates  take gene IDs as input allow you to specify a C<source> option that indicates
182  the type of IDs being used. The acceptable formats are as follows.  the type of IDs being used. The acceptable formats are as follows.
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185    
186  =item CMR  =item CMR
187    
188  L<Comprehensive Microbial Resource ID|http://cmr.jcvi.org>. The CMR IDs for  I<Comprehensive Microbial Resource> (L<http://cmr.jcvi.org>) ID. The CMR IDs for
189  C<fig|272558.1.peg.203> are C<10172815> and C<NTL01BH0204>.  C<fig|272558.1.peg.203> are C<10172815> and C<NTL01BH0204>.
190    
191  =item GENE  =item GENE
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201    
202  =item KEGG  =item KEGG
203    
204  L<Kyoto Encyclopedia of Genes and Genomes|http://www.genome.jp/kegg> identifier.  I<Kyoto Encyclopedia of Genes and Genomes> (L<http://www.genome.jp/kegg>) identifier.
205  For example, the KEGG identifier for C<fig|158878.1.peg.2821> is C<sav:SAV2628>.  For example, the KEGG identifier for C<fig|158878.1.peg.2821> is C<sav:SAV2628>.
206    
207  =item LocusTag  =item LocusTag
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211    
212  =item NCBI  =item NCBI
213    
214  L<NCBI|http://www.ncbi.nlm.nih.gov> accession number. The accession numbers for  I<NCBI> (L<http://www.ncbi.nlm.nih.gov>) accession number. The accession numbers for
215  C<fig|272558.1.peg.203> are C<10172815>, C<15612766>, and C<81788207>.  C<fig|272558.1.peg.203> are C<10172815>, C<15612766>, and C<81788207>.
216    
217  =item RefSeq  =item RefSeq
218    
219  L<NCBI|http://www.ncbi.nlm.nih.gov> reference sequence identifier. The RefSeq  I<NCBI> (L<http://www.ncbi.nlm.nih.gov>) reference sequence identifier. The RefSeq
220  identifier for C<fig|272558.1.peg.203> is C<NP_241069.1>.  identifier for C<fig|272558.1.peg.203> is C<NP_241069.1>.
221    
222  =item SEED  =item SEED
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225    
226  =item SwissProt  =item SwissProt
227    
228  L<SwissProt|http://www.expasy.ch/sprot> identifier. For example, the SwissProt  I<SwissProt> (L<http://www.expasy.ch/sprot>) identifier. For example, the SwissProt
229  identifier for C<fig|243277.1.peg.3952> is C<O31153>.  identifier for C<fig|243277.1.peg.3952> is C<O31153>.
230    
231  =item UniProt  =item UniProt
232    
233  L<UniProt|http://www.uniprot.org> identifier. The UniProt identifiers for  I<UniProt> (L<http://www.uniprot.org>) identifier. The UniProt identifiers for
234  C<fig|272558.1.peg.203> are C<Q9KGA9> and C<Q9KGA9_BACHD>.  C<fig|272558.1.peg.203> are C<Q9KGA9> and C<Q9KGA9_BACHD>.
235    
236  =back  =back

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