MLOGD is a suite of software that detects new protein-coding sequences (CDSs) by analyzing the pattern of mutations across an input sequence alignment. In particular, the software can be used to detect new CDSs that overlap known CDSs in a different reading frame. Such CDSs are difficult to detect with standard gene-finding algorithms. The software is particularly useful for the analysis of virus genome alignments, where overlapping genes and ribosomal frameshifting sites are common.
The Program for Undergraduate Genomics (PGU), funded by the National Science Foundation, is directed at providing undergraduates with the opportunity to experience real research in a lab. Over 50 undergraduate students have been involved in this program in the first three years. These students have come from within the Texas A&M system and as visiting Research Experience for Undergraduates participants from universities in California and Louisiana. PGU students represent some of the very best from the Department of Biochemistry and Biophysics as well as related disciplines such as Genetics and Molecular Biology. For many of these bright students, this has been their first opportunity to do novel research in a real lab situation.
Information and protocols about isolating, purifying, cloning, sequencing, assembling, annotating and analyzing phage genomes
Mauve is a system for efficiently constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion. Multiple genome alignment provides a basis for research into comparative genomics and the study of evolutionary dynamics. Aligning whole genomes is a fundamentally different problem than aligning short sequences. Mauve has been developed with the idea that a multiple genome aligner should require only modest computational resources. It employs algorithmic techniques that scale well in the amount of sequence being aligned. For example, a pair of Y. pestis genomes can be aligned in under a minute, while a group of 9 divergent Enterobacterial genomes can be aligned in a few hours.
Galaxy allows you to do analyses you cannot do anywhere else without the need to install or download anything. You can analyze multiple alignments, compare genomic annotations, profile metagenomic samples and much much more... We provide a public Galaxy instance at http://usegalaxy.org where you can do all this with nothing more than a web browser.