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.).

This service has been moved to
http://discern.uits.iu.edu:8421/view-sequences.html
and the current page will be retired sometime after January 1, 2008.

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
(like 3718 or 6775):

AND/OR a blank- or comma-separated set of explicit chromosomal region specifications
(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 locations is larger than its associated stop locations, 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 sequence origin.
(Positive values will be downstream from the origin; negative values upstream.)

Start at positions from the origin. Stop at positions from the origin.

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.)
It calls the NCBI viewer.fcgi service to fetch sequences from NCBI. (Note that the maximum download size is currently limited to sequences of length less or equal to 2M.)

This software is under development. Please report problems and direct inquiries to Michael Grobe of the Biomedical Applications group within UITS at Indiana University via dgrobe @ iupui.edu.