Human, Mouse, Rat BAC End Sequence Search

Rat BAC ends from CHORI-230 and Mouse BAC ends from RPCI-23 & RPCI-24 are available

Sequences from the ends of bacterial artificial chromosome (BAC) clones provide highly specific markers. A whole-genome sequencing approach has been described to use BAC end sequences in a map-as-you-go strategy. The complete sequence of a seed BAC is searched against a BAC end database and the minimally overlapping clones in each direction are selected.

The current human BAC end database consists of sequences generated by TIGR, UofWashington and CalTech. See README for more information. Mouse BAC ends from librares RPCI-23 and RPCI-24, rat BAC ends from library CHORI-230 generated by TIGR are available for both sequence and clone search. A monthly incremental database containing BAC ends generated in last 30 days has been set up such that users don't have to search the whole set. Users have to be aware that a small fraction of BAC end sequences may not represent the original clones.

This server runs WU-BLAST 2.0. [Disclaimer]

Select a program and database to search against:




Upload a file containing a sequence OR paste it into the textbox:

(Note: If both are entered, the file will be ignored.)

Enter the name of the file containing a sequence in FASTA or raw format:

Enter your sequence in FASTA or raw format:

Sequence identifier (for definition line if raw sequence entered):








Wordlength (for blastn only):


Ignore Hypotheticals

Graphical Overview

Map Overview

PID (map overview only)

The email option allows the user to be notified by email when the blast search is completed. The email will contain a link to the results. Use this option when running a lengthy search. To activate this option, check the box to the left and fill in an email address in the box to the right.

Send a link to results to email address:

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