HMMER is a free and commonly used software package for sequence analysis written by Sean Eddy. Its general usage is to identify homologous protein or...

Stockholm format as do the probabilistic database search tools, Infernal and HMMER, and the phylogenetic analysis tool Xrate. Stockholm format files often...

LLVM-GCC and Clang both struggled to compete with GCC 4.5.0 in the timed HMMer benchmark of a Pfam database search. LLVM-GCC and Clang were about 23% slower(...

Federal Government market. Strand Life Sciences TimeLogic offers DeCypher FPGA-accelerated BLAST, Smith-Waterman, HMMER and other sequence search tools....

2002 (GOR V) Jpred Multiple Neural network assignment from PSI-BLAST and HMMER profiles. Predicts secondary structure and solvent accessibility Webserver...

HHpred / HHsearch free server and software for protein sequence searching HMMER, a free hidden Markov model program for protein sequence analysis Hidden...

Impress STK Stockholm multiple sequence alignment Bioinformatics tools eg HMMER, Xrate, Jalview STL surface geometry of a three-dimensional object software...

simulations. The partners of the project included Oxford University. The HMMER Genetic Research project made use of the Hidden Markov model to search for...

2075, 2090, K10, K20, K20X Single only Available now, version 2.2.26 GPU-HMMER Parallelized local and global search with profile hidden Markov models Parallel...

analysis with Cistrome pipeline (MACS, CEAS, etc.) Raw NGS data processing HMMER 2 and 3 packages integration Chromatogram viewer Search for transcription...

seed alignment is then used to build a profile hidden Markov model using HMMER. This HMM is then searched against sequence databases, and all hits that...

by matching with Hidden Markov Models is a popular alternative, such as HMMER. An alternative to BLAST for comparing two banks of sequences is PLAST....

sequences may be identified by homology search, using tools such as BLAST, HMMER, OrthologR, and Infernal. Homology search tools may take an individual nucleic...

As of 2016[update] projects include the use of Hidden Markov models in HMMER, Infernal Pfam and Rfam. Eddy graduated June, 1982 from Marion Center Area...

sequences. It is developed in Java and open source. Both Albrecht F 2015 HMMER Local and global search with profile Hidden Markov models, more sensitive...

the Sequence Alignment and Modeling System (SAM) software package. and HMMER. SAM has been used as a source of alignments for protein structure prediction...

categories. BLAST BlastCL3 BioGrep ClustalW EMBOSS Genesplicer GlimmerHMM HMMER Modeller PamL Phylip Primer3 R programming language & Bioconductor T-Coffee...

in multiple sequence alignments. MicroRNA homepage RNAmmer RNAmmer uses HMMER to annotate rRNA genes in genome sequences. Profiles were built using alignments...

NCBI Blast through the Blast URLAPI (previously known as QBlast) and the HMMER web service. The need for customized software in the field of bioinformatics...

protein families found in Bacteria and Archaea. Like Pfam, TIGRFAMs uses the HMMER package written by Sean Eddy. TIGRFAMs was produced originally at The Institute...

playing Plays the game of Go, a simply described but deeply complex game. 456.hmmer C Search Gene Sequence Protein sequence analysis using profile hidden Markov...

of the ubiquitous bioinformatics algorithms BLAST, Smith-Waterman, and HMMER using field programmable gate array (FPGA) technology. In 2003, TimeLogic...

an expect value of 0.001 or lower taken to be statistically significant. HMMER or psi-blast searches are used for adding sequences which are distantly...

of false positive predictions and therefore should be used with caution. HMMER 2.3.2 Used for local Pfam Searches Homodeller 2.0 Locally developed homology...

Saccharomyces cerevisiae BLASTP and PSI-BLAST against 18 fungal species, HMMER and HHpred against several databases, TBLASTN against three close relatives...

computing solutions, focusing on accelerating open source algorithms such as HMMER, Smith-Waterman and ClustalW, using FPGA technology. However these products...

Pipeline (PGAP) while sample specific DNA annotation was synthesized using the HMMer suite, OriFinder, TBLASTN, Pfam, TIGRFam, TnpPred, Alien_Hunter, and antiSMASH...

also worked with Sean Eddy to discover novel protein domains using the HMMER software. In 1997, Bateman joined the Wellcome Trust Sanger Institute to...

Nunes VA, Paiva PB, Araujo MS, Sampaio CA. "Kunitz STI inhibitors". A web/HMMer based tool to study Kunitz protease inhibitors. Federal University of São...

several methods dedicated to proteic annotation: Pfam domain prediction using HMMER Several EMBOSS methods (antigenic, 2D structure prediction) Genostar's Expression...