a graphic BLAST cruncher

Summary

The BLAST series of programs (Altschul et al.) were designed to compare nucleotide and peptide sequences with those in sequence databases. They do this in a statistically valid way to produce a series of high scoring pairs (HSPs) which are aligned pairs of sequences from the query and the database (sbjct). HSPs are identified by their loci in the query and sbjct sequences as well as by their similarity scores and percentage identities and similarities.

Output from blast is typically in human readable text format, which is intelligible when the output is of limited size, as is typical for short sequences. However when there are long sequences in the comparison, many HSPs result. For a typical small genome comparison there are typically approximately 10000-20000 HSPs with an output file consisting of several megabytes of text.

CROSS is a Windows 9x/NT program which does the following:

1. read BLAST output (multiple sbjct - multiple query) either from the system clipboard or file,
2. parse the data into HSP lists (scores, query and sbjct loci)
3. presents the data in several interactive forms:
1. Diagonal plot (dot plot)
2. Map plot (positions of query on multiple sbjct lines)
4. Filters the presented data:
1. Minimum - maximum displayed score ranges
2. Color by strand
3. Statistics display (dynamic display of the object under the cursor)
4. Repeat finder (color coded haloes)
5. Indel finder generates lists of gaps in query/sbjct
5. Outputs various data to the system clipboard
1. Graphics - copy and paste (straight into MS Office apps)
2. Text - tab delimited data for spreadsheets (copy and paste to Excel)
1. Hits
2. Indels
3. Sbjct list
4. Repeats

What is not obvious at first is that the different modalities of blast query produce output which translates into information useful for a variety of purposes:

Examples:

Screen Shot of CROSS