Get NCBI sequences for genes or specific regions

Get NCBI sequences for genes or specified regions

This form will submit requests to NCBI to retrieve sequences for named genes, NCBI gene UIDs, and/or explicitly specifed regions (chromosomal, protein, etc.),

Specify an organism name suitable for the Entrez ORGN field (like "mouse" or "human")

that will apply to every name in a blank- or comma-separated list of NCBI gene names
(like JAK3 or STAT4):

AND/OR enter a blank- or comma-separated list of NCBI UID numbers for any species
(like 3718 or 6775):

AND/OR a blank- or comma-separated set of explicit contig region specifications for any species
(like minus strand NC_000019.8:17819799-17797960 or plus strand NC_000019.8:17797960-17819799):

The general form of explicit region specifications is:

     XX_########:start_location-stop_location

where "XX" is one of "NT", "NM", "NC", "NP", etc., "#######" is an integer contig ID, and the start and stop locations are positive integers. If a start location is larger than its associated stop location, the script will understand that a minus strand has been requested, but will return the requested sequence in positive strand order. (Also, base sequences will NOT be returned in reverse complement.)

If desired, modify each request to download bases relative to the most upstream element (usually the sequence origin).
(Postive values will be downstream from the most upstream element; negative values upstream.)

Start at positions from the most upstream element. Stop at positions from the most upstream element.

Sequence specifications will only be validated by default.
Do you want to actually fetch the sequences?
Yes: No:

Data will be displayed on a web page unless you choose to have it downloaded.
Do you want to download sequences to a file?
Yes: No:

Notes:

This program calls NCBI eSearch to convert gene names to gene UIDs.
It calls NCBI eSummary to find sequence contig info for gene UIDs. (Note that provisional sequence contigs will be ignored.)
The maximum sequence length is currently set at 2,000,001 by this program, but viewer.fcgi may impose a smaller limit. The program will check to make sure the number of bytes requested matches the number of bytes received.

This software was originally developed with major support by the Pervasive Technology Institute of Indiana University. Please report problems and direct inquiries to Michael Grobe at grobe @ ku.edu.