Usage: dna_to_fplot [-q -c -dDb1,Db2... ] Dna_file

Runs the most common set of analyses automatically. Genomic DNA is masked, searched against the Genbank databases using BLASTN, searched for exon and other features using GRAIL 2. cDNA sequence is also translated and searched against the nr database. For cDNA sequences, ORF analysis is performed, but GRA IL 2 isn't used. The results of these analyses are combined and displayed as an HTML page using the fplot program. Output files for each analysis is retained. Options:

-c cDNA analyses will be run. Default is genomic sequence.

-dDb1,Db2... Databases to BLAST sequence against. Default is nr, dbest, gss, and htgs.

Example: dna_to_fplot Dna.fasta

This perl program brings together a number of other DNA analysis programs. It runs one set of analyses for genomic sequence, and another set for cDNA sequences.

It's input is a DNA sequence, and it:

1) Masks the DNA, using the GRAIL repeat server, outputting a file of masked DNA and a file of repeats (*.grail.mask and *.grail.repeats).

2) Finds ORFs. (cDNA only).

3) BLASTs the DNA against several databases, outputs files containing the BLAST results.

4) Parses the BLAST results into a text report and an fplot file. For each database search, outputs a text report (*.parse) and a fplot formatted file (*.fplot).

5) Runs the DNA through the GRAIL server to find exons and the other DNA features GRAIL can find. Outputs a exon file (*.grail2.exons) and a file with the other GRAIL results (*.grail2.CpG.pol2,polyA). (genomic sequence only).

6) Runs the results of 1), 3), and 4) through preplot to combine the BLAST result *.fplot files, and import the other result types. The final fplot format file is saved as *.fplot.

7) The final *.fplot file is run through fplot to generate a set of Html pages which display the results using dynamic Html (*.html, *.gif, *.Legend.html).

Last modified: 4/99

Written by Jim Lund in the lab of Roger Reeves, Johns Hopkins University

Diagram of dna_to_fplot analyses