I just learned about this one: ROSALIND is a really cool concept in learning bioinformatics. You are given problems of increasing difficulty to solve. Start with nucleotide counting (trivial) and end with genome assembly (not so trivial). To solve a problem, you download a sample data set, write your code and debug it. Once you think you are ready, you have a time limit to solve and provide an answer for the actual problem dataset. If you mess up, there is a timed new dataset to download. This thing is coder-addictive. Currently in Beta, but a lot of fun and seems stable.
Analysis of microbial genomes often requires the general organization and comparison of tens to thousands of genomes both from public repositories and unpublished sources. MicrobeDB provides a foundation for such projects by the automation of downloading published, completed bacterial and archaeal genomes from key sources, parsing annotations of all genomes (both public and private) into a local database, and allowing interaction with the database through an easy to use programming interface.
Web-based program Mojo Hand for designing TAL and TALEN constructs for genome editing applications (www.talendesign.org). The precise algorithm and its implementation is described. The features of Mojo Hand include (1) automatic download of genomic data from the National Center for Biotechnology Information, (2) analysis of any DNA sequence to reveal pairs of binding sites based on a user-defined template, (3) selection of restriction enzyme recognition sites in the spacer between the TAL monomer binding sites including options for the selection of restriction enzyme suppliers, and (4) output files designed for subsequent TALEN construction using the Golden Gate assembly method.
MicroRNAs constitute a hitherto unexplored layer of genetic interactions between the virus and the host. The regulatory impact of microRNAs is huge because a single microRNA can regulate multiple transcripts and multiple microRNAs can regulate a single transcript.