[BioC] ASN.1

[Ben Tupper]

Hello,

We make extensive use of NCBI's blast application [1] in our workflows.  One of the optional output formats of the application is XML formatted data.  That output works very well for most of our purposes as this form of output is complete. However, we have encountered an issue where, for very large inputs, output to XML becomes very resource heavy for our server - bring our workflow to a crawl.  We are trying end-runs around the issue including using other output format options (flat ascii tables, html, etc.), and also by saving the output to NCBI's ASN.1 archive format [2] and then converting using the blast_formatter application [3] but none fit the bill. 

NCBI makes its AsnLib tool kit available, but don't have the resources at this time to dive into C and C++.  We are wondering if there are any resources available in R for reading NCBI's ASN.1 archive format.  Do such beasts exist?

Thanks,
Ben

[1] http://www.ncbi.nlm.nih.gov/books/NBK1763/
[2] http://www.ncbi.nlm.nih.gov/IEB/ToolBox/SDKDOCS/ASNLIB.HTML 
[3] http://home.cc.umanitoba.ca/~psgendb/birchhomedir/doc/NCBI/blast_formatter.txt



Ben Tupper
Bigelow Laboratory for Ocean Sciences
180 McKown Point Rd. P.O. Box 475
West Boothbay Harbor, Maine   04575-0475 
http://www.bigelow.org