They are actually two separate sets of protein entries. In order to emulate an IPI database, you would need to download both and concatenate them.
IPI, though, is species specific, so if your search engine does not support auto-filtering of entries by taxonomy, you will need to pre- filter the entries on species. The easiest way to do this is to query uniprot for species and then use the download link on the right hand side of the result page to get the FASTA file. step 1: https://skitch.com/delagoya/rrfwu/uniprot-query-1 step 2: https://skitch.com/delagoya/rrfww/uniprot-query-2 step 3: https://skitch.com/delagoya/rrfw3/uniprot-query-3 step 4: https://skitch.com/delagoya/rrfib/uniprot-query-4 step 5: https://skitch.com/delagoya/rrfix/uniprot-query-5 Step 5 involves choosing whether you want the isoforms included in your search database. On Dec 9, 2:34 am, good man <[email protected]> wrote: > As IPI (International Protein Index) database has closed, and they > recommend the use of UniProtKB as the reference database for mass > spectrometry in future. But I don't know exactly which one to choose: > UniProtKB/Swiss-Prot , UniProtKB/TrEMBL and UniRef. I feel so confused > about the databases in UniProtKB. > There are also NR database in NCBI reference sequences (RefSeq). > Would anyone tell me which one is the best? > Thank you! -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
