publications, web-pages, and presentations related to the Jrna web-site

• Gillespie, Yoder, and Wharton. 2005 . Predicted secondary structures for expansion segments D2-D10 of the 28S large subunit rRNA from Ichneumonoidea (Insecta: Hymenoptera: Apocrita): Homology assignment and phylogenetic implications. Journal of Molecular Evolution.
• Munro, Gillespie, Heraty, Yoder, Owen, and Carmichael. 2004. A secondary structural model of the 28S rDNA expansion segments D2 and D3 from Chalcid wasps (Hymenoptera: Chalcidoidea): Implications for multiple sequence alignment and phylogeny reconstruction. Section A Student Competition Poster. ESA Annual meeting. (~3mb)
• Gillespie, Yoder. 2004. New structure-based methods for the phylogenetic analysis of ribosomal RNA sequences using the parsimony optimality criterion. Section A Talk. ESA Annual meeting. (~650kb)
• Yoder, Gillespie. 2004. Seeded multiple sequence alignment of rRNA encoding genes for the purposes of phylogenetic study. Section A Poster. ESA Annual meeting. (~400kb)
• Yoder, Gillespie. 2004. Towards the use of morphological characters based on RNA secondary structure in revisionary systematics. PEET V. University of Illinois at Urbana-Champaign.
• Yoder, Gillespie. 2004. Perl scripted manipulation of RNA multiple sequence alignments. International Congress of Entomology, Brisbane. (powerpoint presentation) (~6mb)

rna on the world-wide-web

• The RNA World
• Comparative RNA Web Site
• European RNA Database
• Ribosomal Database Project
• www.bioinformatics.vg -links
• BRAliBase: Benchmark RNA Alignments. -links
• RNA Studio at BibiServ
• The RNase P Database

summary pages (these are likely better than this set of links)

• iUBio archive at U. Indiana
• Ian Holme's multiple alignment summary page
• MEG's (University of Copenhagen) list of RNA utilities

servers

• mfold
• pfold

individual utilities

• Assemble homepage. Very nice.
• DART homepage at sourceforge
• RNAVIZ seems to be down now
• XRNA visualization
• RNAView, RNAmlView visualization from the nab lab at Rutgers
• RNAsoft can simulate sequences based on a mask

labs working with RNA

no association implied- these folks just do cool stuff!

• Homepage of Sean Eddy (Eddy Lab)
• Homepage of Paul Gardner
• Homepage? of Ian Holmes
• Homepage of Jotun Hein
• Doug Turner Group

perl

• bioperl
• Perl on Windows
• perlmonks

TAMU

• hymenoptera.tamu.edu
• Holistic Insect Systematics Laboratory
• TAMU Dept. of Entomology
• tamu

This page is a joint project of NSF PEET grants DEB-0328922, DEB-0328920, and DEB-9978150 ; ideas and opinions expressed here are those of the authors, and not the NSF; best viewed with Firefox, Mozilla, or OS X Safari. This material is copyright and may not be reproduced without permission. Last modified: March 04 2014 12:04:08. Svedberg Site usage tracked by google analytics.