[EMBOSS] Question regarding dbxflat

Jean Mao maoj at helix.nih.gov
Tue Oct 17 15:36:22 UTC 2006


Could someone help me determine which fields I need to include while running dbxflat? I am going to index the genbank and est gb*.seq files and gbest*.seq files from ftp://ftp.ncbi.nih.gov/genbank/. These files have sequence entries composed of : Locus, Definition, Accession, Version, Keywords, Source, Organism……

If I specify 'acc, id' while indexing, will the 'Definition' line be indexed or not? What about 'acc, id, des' ? In other words, I would like to know which programs in EMBOSS will not work if I don't specify 'des' while indexing. 
Some programs in EMBOSS such as 'coderet' require feature table. If I only index 'acc, id', will coderet work when user specify 'genbank:xxxxx' ?

I guess all I am trying to ask is what programs will stop working if I only accept default 'acc, id' fields.

Thank you in advance.

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