BatchSearch < FIG

FIG Web>HelpIndex > NmpdrSearch > NmpdrSearchTypes>BatchSearch

The Batch Search is not technically a search in the normal sense; rather, it allows you to upload a list of feature IDs and see them as Search Results. The IDs can be standard FIG IDs or any of the recognized aliases.

As an alternative to uploading, you can copy the IDs and paste them into the text box below the upload control. You can use both capabilities if, for example, you have a file and want to add some IDs to it.

Both ID lists can be in any of several formats. You can specify the IDs as comma-separated values (with or without quotes), tab-delimited, space-delimited, or one per line. Blank lines are ignored. You can freely mix the formats in a single file, as shown below.

fig|158878.1.peg.258
luxR
"fig|155879.1.peg.1382", "gi|57020922", "CFF8240_0789"

CCO0860 LocusTag:CJE0892 LocusTag:TC0872

Because this is a feature search, when the results come back you can download them in FASTA Format or view them in an Interactive Table. This ability is the most common reason for doing a batch search.

The default operating mode of the batch search is to return all IDs in the input file. If, however, you know the genomes in which you are interested, you can select them in the Genome Control in the input form. This will insure that names which are not unique between genomes (such as locus tags) return correct results.

The presumption is that each ID in the input file will produce one search result, but this does not always happen. In our sample file above, the ID luxR is a protein name that matches three genes, and there is no feature with the name fig|155879.1.peg.1382. The batch searcher will display this information in the results, as shown at left.

The Batch Search can be found here.

Topic revision: r5 - 31 Mar 2009 - 18:49:08 - Bruce Parrello

Notice to NMPDR Users - The NMPDR BRC contract has ended and bacterial data from NMPDR has been transferred to PATRIC (http://www.patricbrc.org), a new consolidated BRC for all NIAID category A-C priority pathogenic bacteria. NMPDR was a collaboration among researchers from the Computation Institute of the University of Chicago, the Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the National Center for Supercomputing Applications (NCSA) at the University of Illinois. NMPDR is funded by the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under Contract HHSN266200400042C. Banner images are copyright © Dennis Kunkel.