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Choose program to use and database to search:

Program Database

Enter sequence below in FASTA format

Or load it from disk

Set subsequence: From To

The query sequence is filtered for low complexity regions by default.
Filter Low complexity Mask for lookup table only

Expect Matrix Perform ungapped alignment

Query Genetic Codes (blastx only)

Database Genetic Codes (tblast[nx] only)

Frame shift penalty for blastx

Other advanced options:

Graphical Overview Alignment view
Descriptions Alignments Color schema


For your convenience we offer a web interface to Blast against all of our fosmid ends.

The fosmid end databases are available only in an "nt" version. This corresponds to the nt sequence of each fosmid end we have sequenced for a particular organism. Please note that each blast program has different requirements for nucleotide or amino acid input and databases. The following table is a guide:

Program Input Database
blastn nt
tblastn aa nt
tblastx nt


The "Fosmid_Ends" database includes all end sequences from all fosmid libraries created by this project.  There are also organism-specific fosmid ends databases available.