Search Results for "hmmer"

Modified HMMER that can utilize databases split across compute nodes, as opposed to using one large database on the master node and moving all of the data across the network on each run. Also implements a web server interface which is aware of these changes.

...If the user inputs a complete proteome, additional modules evaluate the completeness of the kinome and place it in context with reference kinomes. Kinannote runs on a unix command line and depends on local hmmer 2 and Blast 2.24 installations. Citing Kinannote: Kinannote, a computer program to identify and classify members of the eukaryotic protein kinase superfamily Jonathan M. Goldberg; Allison Griggs; Janet L. Smith; Brian Haas; Jennifer Wortman; Qiandong Zeng Bioinformatics 2013; doi: 10.1093/bioinformatics/btt419 http: http://bioinformatics.oxfordjournals.org/content/29/19/2387.full pdf: http://bioinformatics.oxfordjournals.org/content/29/19/2387.full.pdf+html

Genix is an online automated pipeline for bacterial genome annotation that integrates the programs Prodigal, BLAST, RNAmmer, tRNAscan-SE, INFERNAL, ARAGORN and HMMER, and the databases Uniprot, Antifam and Rfam.

...In addition to the increase in image size (less than 2 gigabytes) and a new Linux base (previously Debian, now Ubuntu), CUDA-capable bioinformatics software programs, such as NAMD, HOOMD-blue, VMD, GPU-HMMER and GPU-BLAST, are pre-installed in birgHPCC, along with the CUDA driver, libraries and software development kit (SDK). In short, birgHPCC is the world's first CUDA-ready, bioinformatics-based, live DVD.

metaProt is a python pipeline to analyze and extract data from protein sequences found in metagenomic projects. It integrates several existing tools (HMMer, Pepstats, Blast...) to be used against custom databases. Please, read the README.txt file to find more about this.

hmm2gviz is a tool used for converting hidden Markov models generated by HMMER into a graph visualization using Graphviz.

Here we offer for download ClawHMMer, a streaming implementation of hmmsearch, running on commodity graphics. processors and parallel rendering clusters. The original HMMer version is located at http://hmmer.wustl.edu/ (also under GPL).