How to view a transcriptome scaffold...

[MetteHHH]

Hello SeqAnswers community,

A collaborator just sent me a transcriptome scaffold: He suggests that we try to BLAST a set of mapped genetic markers against it to link our markers to the transcriptome.

The tar file he sends contains a fasta file and a txt file. The text file is divided into sections, each labelled with a contig number and containing five columns: First a column with an identifier, then a column with a number, another identifier, another number, and finally a column with an abbreviation, which is either "FP" or (more rarely) EXP_GAP or EXP_JCT

Does anyone recognize this format? I assume that the .txt file allows the FASTAs to be assembled into a scaffold, but I am a bit lost as to what software to use. Could anyone point me to a (preferably UNIX-based) resource?

Thanks a million in advance!
Mette

[MetteHHH]

...I might add that I figured out most of the contents of the .txt file (I believe). So, within each section, the first column is a clone ID (corresponding to an identifier in the fasta file), the second column is the read length; third column is the ID of the next overlapping clone, and the fourth column is the position (in the first read) of of the first overlapping base of the second read. Hope that makes sense. Still did not figure out what the abbreviation in the fifth column means...

That ought to mean that I could possibly assemble this scaffold into contigs using some home brewed awk-script... but I'm sure there must be tools out there...?