Hordeum vulgare Genome DB

Data Sets, Methods, and Resources

HvGDB encompasses primary sequence data obtained from GenBank, including the most current gss and BAC assembly and annotation, EST and cDNA sequences, and protein sequences derived from the annotated genes. Hordeum vulgare genome assemblies refer to the pseudo-chromosome tiling of individual genomic sequence fragments obtained from the listed assembly sources. The mapping of cDNA and EST sequences onto the genome as well as interpretations of the overall data are based on our own spliced alignment results.

The barley genome assembly is still being refined and completed. HvGDB attempts to remain synchronized with the most recent release of the genome assembly and annotations.

Hordeum vulgare BAC Genome

Data Sets

BAC Genomic Sequences:
59 barley BAC-size (>= 10 kb) sequences were obtained from PLN and HTG division of GenBank release 157.

Transcript Sequences:
463088 transcript sequences from EST, PLN and HTC division were obtained from GenBank release 157.

Methods

GeneSeqer
GeneSeqer is a gene identification tool based on spliced alignment or "spliced threading" of cDNAs/ESTs into a genomic DNA sequence template.

Resources

NCBI BLAST
Stand-alone (local) BLAST is a pairwise alignment search tool used for sequence-based querying of on-site databases.

MySQL
MySQL is "the world's most popular Open Source Database, designed for speed, power and precision in mission critical, heavy load use."

Apache
The Apache HTTP Server Project is "an effort to develop and maintain an open-source HTTP server for modern operating systems including UNIX and Windows NT. Apache has been the most popular web server on the Internet since April of 1996."

Perl
A web site without it just isn't a web site at all!

Perl::CGI.pm
This perl 5 library "uses objects to create Web fill-out forms on the fly and to parse their contents. It provides a simple interface for parsing and interpreting query strings passed to CGI scripts. However, it also offers a rich set of functions for creating fill-out forms. Instead of remembering the syntax for HTML form elements, you just make a series of perl function calls. An important fringe benefit of this is that the value of the previous query is used to initialize the form, so that the state of the form is preserved from invocation to invocation."

Perl::GD.pm
Graphics on-the-fly just wouldn't be the same without it!

Links

Data Sets, Methods, and Resources