gnomap (version 2 alpha, May 2002) for simple, efficient genome map production from command-line systems d. gilbert, email@example.com
gnomap is designed read various genome annotation data, draw a simply formatted display of it with Java graphics methods, then dump that out into a graphics file in common formats, including GIF, PNG, PDF, and PS, the first two being bitmapped, suitable for web browser displays, the later two are vector graphics with more uses including print and document publications.
It is used primarily in web servers at euGenes and Flybase (as /.bin/gnomap) to provide a simple, effective way for scientists to view and locate genes and other annotation features on the large quantity of data from genomes of human, fruitfly, worm and other organisms.
Version 1 of gnomap was optimized to use a simple but specific text database format that can be generated from the variety of extant genome data. See feature format and here for example feature dataset. gnomap also reads a range of standard biosequence formats via Readseq software, though this is less efficient.
Version 2 of gnomap is extending the range of inputs to include DAS and LDAP directory services for genome data. For test drives of version 2 with remote data, try this form.
More details of gnomap v.2 are found in gnomap help, and the source code, plus scripts to use, are in gnomap.v2a.tar.gz
LDAP directories may offer a wide range of bio-data directory services, using existing protocols and relatively mature software. Servers and clients for LDAP browsing, search and retrieval are commonly available, and hooking in biology data takes not much more effort than writing interfaces to existing bio-databases.
If you are interested in LDAP and DAS for distributed directories of bio-data, see das2ldap, which is a LDAP-backend server adapted from the LDasServer. Source to install your own DAS-LDAP gateway is in das-slapd.tar.gz