Conserved Domain Batch Retrieval

Question

[bran10.sp]

I need to do a batch retrieval of conserved domain of nearly 400+ plant toxic protein sequence...Need tool suggestions..ASAP..Conserved domain in pictorial representation..

Answer 1

[Elisabeth Gasteiger]

Do you have UniProt identifiers? In that case, you could use the "Retrieve" tab on the UniProt web site, http://www.uniprot.org If the domains you are looking for are annotated in UniProtKB/Swiss-Prot, you might find the instructions given in this FAQ useful: http://www.uniprot.org/faq/50

If you have any questions concerning the use of the UniProt web site, please do not hesitate to contact [e-mail]

Answer 2

[Min Dai]

You can try Batch CD-Search from NCBI: https://www.ncbi.nlm.nih.gov/Structure/bwrpsb/bwrpsb.cgi.

Batch CD-Search serves as both a web application and a script interface for a conserved domain search on multiple protein sequences, accepting up to 4,000 proteins in a single job. It enables you to view a graphical display of the concise or full search result for any individual protein from your input list, or to download the results for the complete set of proteins. The Batch CD-Search Help provides additional details. (https://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml)

Also SMART database offers a section for precomputed results batch retreival: http://smart.embl.de/smart/batch.pl.

Enter a list of sequence identifiers, separated by newlines. Use standard Swiss-Prot or Ensembl style IDs or ACCs. You can also paste a set of sequences in FASTA format. There is a limit of 10000 sequences per access. You will only get results for sequences that have a match in SMART database, ie. only precomputed results will be displayed.

[lessismore]

Hi Minstein, can you please have a look at this question? Conserved Domain analysis (CD-search)