Data Sets, Methods, and Resources
PpGDB encompasses primary scaffold data obtained from JGI,EST and cDNA sequences from GenBank and protein sequences derived from
the annotated genes.
Physcomitrella patens 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 moss genome assembly is still being refined and completed.
PpGDB attempts to remain synchronized with the most recent release of the
genome assembly and annotations.
Physcomitrella patens BAC Scaffold
Data Sets
Genomic Sequences:
2106 moss scaffolds were obtained from JGI release version 1_1.
Transcript Sequences:
326457 transcript sequences from EST, PLN and HTC division were obtained from GenBank release 163.
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!
© 2006 Shannon D. Schlueter