About HMMER — HMMER web server 1.0 documentation

The HMMER project is a collaborative project between the HMMER algorithm developers, led by Sean Eddy at HHMI/Harvard University and the HMMER web service team, lead by Rob Finn at EMBL-EBI. The software is available at hmmer. While the HMMER algorithm developers focus on improving the speed and sensitivity of searches, the …

Modern Computational Techniques for the HMMER …

This paper focuses on the latest research and critical reviews on modern computing architectures, software and hardware accelerated algorithms for …

yuanj82/auto-hmmer: Automated hmmer retrieval program.

Automated hmmer retrieval program. Contribute to yuanj82/auto-hmmer development by creating an account on GitHub.

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HMMER web server: interactive sequence similarity searching

HMMER. BLAST. Comments.; Program: phmmer: blastp: Produces similar results in terms of homolog detection. Searching with the sequence from PDB ID 2abl, chain A against PDB yields 244 matches compared with 214 matches for phmmer and blastp, respectively, using an E-value threshold of 0.01 and default search parameters.The …

HMMER User's Guide

HMMER can be used to search sequence databases with single query sequences but it becomes particularly powerful when the query is an alignment of multiple instances of a sequence family. HMMER makes a profile of the query that assigns a position-specific scoring system for substitutions, insertions, and deletions.

HMMER3 · bio.tools

HMMER is a software suite for protein sequence similarity searches using probabilistic methods. Previously, HMMER has mainly been available only as a computationally intensive UNIX command-line tool, restricting its use. Recent advances in the software, HMMER3, have resulted in a 100-fold speed gain relative to previous versions. ...

HMMER

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HMMER

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HMMER — pyhmmer 0.10.8 documentation

hmmsearch¶ pyhmmer.hmmer. hmmsearch (queries, sequences, cpus = 0, callback = None, ** options) ¶ Search HMM profiles against a sequence database. In HMMER many-to-many comparisons, a search is the operation of querying with profile HMMs a database of sequences.. The hmmsearch function offers two ways of managing the database that will …

hmmer+blast (hmmer)

hmmer+blast (hmmer) . hmmsearch + blast. . hmmsearch,pfam,,,. blast ...

hmmer

HMMER is the official website of HMMER, a powerful tool for finding and aligning sequences with profile hidden Markov models. HMMER provides information on how …

HMMER Manual | i5k

When the HMMER program has finished, your results will be displayed. In 'Download' you can download the input file, the HMMER result (showed in 'Report Details') and the submission details including parameters used in this job. In 'Report Details', reports are separated into independent sections by protein datasets. Use the drop-down list to ...

HMMER

We believe HMMER compiles and runs on any POSIX-compliant system with an ANSI C99 compiler, including Mac OS/X, Linux, and any UNIX operating systems, provided it supports SSE2, ARM NEON, or big-endian Altivec/VMX vector instructions. This includes essentially all Intel/AMD compatible machines, Apple OS/X Intel or ARM machines, and some …

index about | HMMER

The HMMER project is a collaborative project between the HMMER algorithm developers, led by Sean Eddy at HHMI/Harvard University, and the HMMER web service team, lead by Rob Finn at EMBL-EBI . Between us, we aim to provide Life science researchers fast and sensitive homology searches, which are accessible to the broadest possible community.

HMMER3.1

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HMMER User's Guide

sequence alignments. HMMER can be used to search sequence databases with single query sequences but it becomes particularly powerful when the query is a multiple …

HMMER web server: interactive sequence similarity searching

Abstract. HMMER is a software suite for protein sequence similarity searches using probabilistic methods. Previously, HMMER has mainly been available only as a computationally intensive UNIX command-line tool, restricting its use. Recent advances in the software, HMMER3, have resulted in a 100-fold speed gain relative to previous …

The HMMER Web Server for Protein Sequence Similarity Search

The HMMER Web server provides a common platform by linking the HMMER algorithms to databases, thereby enabling the search for homologs, as well as providing sequence and functional annotation by linking external databases. This unit describes three basic protocols and two alternate protocols that explain how to use the …

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Complete Guide: Installing hmmer on Ubuntu 22.04 LTS …

This guide covers the steps necessary to install hmmer on Ubuntu 22.04 LTS (Jammy Jellyfish) $ sudo apt update $ sudo apt install hmmer. 2. Uninstall "hmmer" package. Here is a brief guide to show you how to uninstall hmmer on Ubuntu 22.04 LTS (Jammy Jellyfish): $ sudo apt remove hmmer $ sudo apt autoclean && sudo apt …

HMMER web server: 2018 update

The HMMER website now provides a single point of entry for those wishing to access the profile HMM libraries supported by EMBL-EBI. The profile HMM libraries have been updated as newer versions became available (Pfam to version 31.0 and CATH-Gene3D to 16.0.0). We have updated the different post-processing procedures that …

HMMER web server: interactive sequence similarity searching

HMMER is a software suite for protein sequence similarity searches using probabilistic methods. Previously, HMMER has mainly been available only as a computationally intensive UNIX command-line tool, restricting its use. Recent advances in the software, HMMER3, have resulted in a 100-fold speed gain …

Now Available: NCBI Hidden Markov Models (HMM) Release …

Search this collection against your favorite prokaryotic proteins to identify their function using the HMMER sequence analysis package. What's new? Release 14.0 contains: 16,383 HMMs maintained by NCBI; 252 new HMMs since release 13.0 ; Several hundreds HMMs with better names, EC numbers, Gene Ontology (GO) terms, gene …

hmmscan search | HMMER

There are three different ways of controlling which HMMs match your query. E-value: Control both significant and reporting thresholds for the model and each hit, 10≥x>0. May be entered with scientific notation.Bit score: Control both significant and reporting thresholds for the model and each hit, x>0.

HMMERBUILD

HmmerBuild provides a Accelrys GCG (GCG) interface to the hmmbuild program of Dr. Sean Eddy's HMMER package. It allows you to access most of hmmbuild's parameters from GCG command line. HmmerBuild creates a profile hidden Markov model from a group of aligned sequences. A profile HMM is a mathematical model that represents the primary …