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NCBI C++ Toolkit Dec 31 2008 (Default branch)

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Special Forums News, Links, Events and Announcements Software Releases - RSS News NCBI C++ Toolkit Dec 31 2008 (Default branch)
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Old 12-31-2008
NCBI C++ Toolkit Dec 31 2008 (Default branch)
The NCBI C++ Toolkit provides portable libraries and applications for assisting genetic science. These include libraries for networking, SQL and BerkeleyDB access, CGI and HTML handling, ASN.1 and XML handling, sequence alignment engines, sequence retrieval engines, BLAST database engines, FLTK and OpenGL graphics toolkits, and basic system utilities. License: Public Domain Changes:
This release adds a method to compute column-specific pseudocounts in PSI-BLAST. It refactors the grid services library. It adds unit test framework and error logging for all File API classes. It fixes pthread support on IRIX. It enhances support of XML serialization. It fixes support for Sybase. It adds support for smaller lookup tables for small queries. It adds an API to retrieve GenBank loader statistics. It has assorted other enhancements, speedups, and bugfixes. Image

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LEARN ABOUT DEBIAN

gbseqget

GBSEQGET(1)						     NCBI Tools User's Manual						       GBSEQGET(1)

NAME

       gbseqget - format sequences from GenBank as an XML GBSet

SYNOPSIS

       gbseqget [-] [-d filename] [-i filename] [-m n/p/b] [-n] [-o filename] [-v]

DESCRIPTION

       gbseqget  retrieves  biological sequence data from GenBank (according to an input list of GI accession numbers) and prints it out as an XML
       GBSet document.

OPTIONS

       A summary of options is included below.

       -      Print usage message

       -d filename
	      Input file name for date list (desired accessions, one per line, followed by a blank line and a list of allowed dates, also one  per
	      line)

       -i filename
	      Input file name for GI list (default = stdin)

       -m n/p/b
	      Molecule type:
	      n      Nucleotide (default)
	      p      Protein
	      b      Both

       -n     Return only new records (for which the given GI refers to an old version)

       -o filename
	      Output file name for the XML GBSet (default = stdout)

       -v     Fetch SNP Variations

NOTES

       The GBSet format is deprecated in favor of INSDSet, which you can produce by running insdseqget in place of gbseqget.

AUTHOR

       The National Center for Biotechnology Information.

SEE ALSO

       asn2gb(1), insdseqget(1).

NCBI
								    2006-04-14							       GBSEQGET(1)