> Tag > Links tagged with 'sequence alignment'

Links tagged with 'sequence alignment'

RSS Feed Compact View Sort by Links Directory Index
downloadList as XML List as JSON List as TSV List as CSV

Found 265 links

Displaying 15 links

Hide Resources (8)Hide Databases (41)Hide Tools (216)

Meta-BASICTool Content

http://basic.bioinfo.pl/ [open in a new window]

Share This Link
Protein > 2-D Structure Prediction
Sequence Comparison > Similarity Searching and Classification

Meta-BASIC is a tool for detecting distant homologues using meta-profiles which combine both sequence positional variability and secondary structure.

links directory index: 85
TitlePublication YearGoogle Scholar Citation Count
Detecting distant homology with Meta-BASIC200485
NAR Web Server Issue 2004
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsalgorithms amino acid sequence homology glycosyltransferases molecular models protein sequence analysis protein structural homology proteins secondary protein structure sequence alignment trna methyltransferases

Meta-MEMETool Content

http://metameme.sdsc.edu/ [open in a new window]

Share This Link
DNA > Structure and Sequence Feature Detection
Protein > Domains and Motifs

Creates hidden Markov model of motif from MEME output and searches sequence database for matches to this motif.

links directory index: 223
TitlePublication YearGoogle Scholar Citation Count
Meta-MEME: motif-based hidden Markov models of protein families1997223
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsalcohol dehydrogenase algorithms amino acid sequence amino acid sequence homology factual databases ferredoxins markov chains molecular sequence data proteins sequence alignment stochastic processes

MetaBioMEDatabase Content

http://metasystems.riken.jp/metabiome/ [open in a new window]

Share This Link
Protein > Databases

MetaBioiME is a web resource to find novel homologs for known Commercially Useful Enzymes (CUEs) in metagenomic datasets and completed bacterial genomes.

This content is being maintained by tdtaylor.

links directory index: 11
TitlePublication YearGoogle Scholar Citation Count
MetaBioME: a database to explore commercially useful enzymes in metagenomic datasets201011
NAR Database Issue 2010
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsanimals bacterial genome computational biology genetic databases humans natural language processing nucleic acid databases open reading frames protein databases sequence alignment tertiary protein structure viral genome

mGenomeSubtractorTool Content

http://bioinfo-mml.sjtu.edu.cn/mGS/ [open in a new window]

Share This Link
Model Organisms > Microbes
Sequence Comparison > Comparative Genomics

mGenomeSubtractor performs mpiBLAST-based comparison of reference bacterial genomes against multiple user-selected genomes. Such in silico subtractive hybridization also allows for definition of species-specific gene pools and can be used to develop genomic arrays.

links directory index: 12
TitlePublication YearGoogle Scholar Citation Count
mGenomeSubtractor: a web-based tool for parallel in silico subtractive hybridization analysis of multiple bacterial genomes201012
NAR Web Server Issue 2010
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsbacterial genes bacterial genome genomics oligonucleotide array sequence analysis sequence alignment species specificity

Microbial Genome Database (MBGD)Database Content

http://mbgd.genome.ad.jp/ [open in a new window]

Share This Link
Model Organisms > Databases

The microbial genome database (MBGD) for comparative analysis is a platform for microbial comparative genomics based on automated ortholog group identification. A prominent feature of MBGD is that it allows users to create ortholog groups using a specified subgroup of organisms. Advanced functionalities include: (i) enhanced assignment of functional annotation, including external database links to each orthologous group, (ii) interface for choosing a set of genomes to compare based on phenotypic properties, (iii) the addition of more eukaryotic microbial genomes (fungi and protists) and some higher eukaryotes as references and (iv) enhancement of the MyMBGD mode, which allows users to add their own genomes to MBGD and now accepts raw genomic sequences without any annotation (in such a case, it runs a gene-finding procedure before identifying the orthologs).

links directory index: 19
TitlePublication YearGoogle Scholar Citation Count
MBGD update 2010: toward a comprehensive resource for exploring microbial genome diversity201019
NAR Database Issue 2010
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsanimals bacterial genome computational biology fungal genome genetic databases genomics humans nucleic acid databases phylogeny protein databases sequence alignment tertiary protein structure

MIGenAS ToolkitTool Content

http://www.migenas.org/ [open in a new window]

Share This Link
DNA > Phylogeny Reconstruction
DNA > Sequence Retrieval and Submission
Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Localization and Targeting
Protein > Phylogeny Reconstruction
Protein > Sequence Retrieval
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments
Sequence Comparison > Similarity Searching and Classification

Max-Planck Integrated Gene Analysis System (MIGenAS) provides access to many different bioinformatics software tools and databases for sequence similarity searching, multiple sequence alignments, phylogenetic analysis, and protein structure prediction. Users can also configure \"meta\"-tools as a pipeline of individual tools and intermediate filters.

links directory index: 16
TitlePublication YearGoogle Scholar Citation Count
The MIGenAS integrated bioinformatics toolkit for web-based sequence analysis200616
NAR Web Server Issue 2006
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsanimals computational biology genetic databases humans mice sequence alignment sequence analysis systems integration

MINERTool Content

http://coit-apple01.uncc.edu/MINER/ [open in a new window]

Share This Link
Protein > 3-D Structure Retrieval/Viewing
Protein > Annotation and Function
Protein > Phylogeny Reconstruction
Sequence Comparison > Analysis of Aligned Sequences

MINER is a tool for the identification and visualization of phylogenetic motifs (regions within a multiple sequence alignment (MSA) that conserve the overall phylogeny of the complete family).

links directory index: 69
TitlePublication YearGoogle Scholar Citation Count
MINER: software for phylogenetic motif identification200517
Predicting protein functional sites with phylogenetic motifs200552
NAR Web Server Issue 2005
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsamino acid motifs base sequence binding sites chemical models computational biology conserved sequence cytochrome p-450 enzyme system false positive reactions fungal proteins molecular evolution molecular models phylogeny protein binding protein conformation protein databases protein sequence analysis proteins proteomics saccharomyces cerevisiae sequence alignment succinate dehydrogenase

MITOPREDTool Content

http://bioinformatics.albany.edu/~mitopred/ [open in a new window]

Share This Link
Protein > Annotation and Function

MITOPRED uses Pfam domains, pI values and amino acid composition to predict nuclear-encoded mitochondrial proteins. Predictions have been precomputed for a number of proteomes, as well as for all Eukaryotic sequences in Swiss-Prot and TrEMBL. Users may directly enter or upload a file with a list of protein sequences or Swiss-Prot/TrEMBL accession numbers.

links directory index: 161
TitlePublication YearGoogle Scholar Citation Count
MITOPRED: a web server for the prediction of mitochondrial proteins200451
MITOPRED: a genome-scale method for prediction of nucleus-encoded mitochondrial proteins2004110
NAR Web Server Issue 2004
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsalgorithms animals cell nucleus gene expression profiling genome humans mitochondrial proteins protein databases protein sequence analysis proteome reproducibility of results sensitivity and specificity sequence alignment software design tertiary protein structure tissue distribution

ModBaseDatabase Content

http://salilab.org/modbase [open in a new window]

Share This Link
Protein > Databases

ModBase is a database of annotated comparative protein structure models. The models are calculated by ModPipe, an automated modeling pipeline that relies primarily on Modeller for fold assignment, sequence-structure alignment, model building and model assessment. ModBase allows users to update comparative models on demand, and request modeling of additional sequences through an interface to the ModWeb modeling server. Recently developed associated resources include the SALIGN server for multiple sequence and structure alignment, the ModEval server for predicting the accuracy of protein structure models, the PCSS server for predicting which peptides bind to a given protein and the FoXS server for calculating and fitting Small Angle X-ray Scattering profiles.

links directory index: 36
TitlePublication YearGoogle Scholar Citation Count
ModBase, a database of annotated comparative protein structure models, and associated resources201136
NAR Database Issue 2011
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
external linksLink on Wikipedia
tagsbacterial proteins molecular models peptides protein databases protein interaction mapping protein structural homology proteins sequence alignment small angle scattering tertiary protein structure x-ray diffraction

ModelTest SeverTool Content

http://darwin.uvigo.es/software/modeltest_server.html [open in a new window]

Share This Link
DNA > Phylogeny Reconstruction

ModelTest is program for the selection the model of DNA evolution (nucleotide substitution) that best fits your data from phylogenetic analyses.

links directory index: 13810
TitlePublication YearGoogle Scholar Citation Count
ModelTest Server: a web-based tool for the statistical selection of models of nucleotide substitution online2006155
MODELTEST: testing the model of DNA substitution199813655
NAR Web Server Issue 2006
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsalgorithms base composition bayes theorem biological models dna dna sequence analysis genetic variation likelihood functions molecular evolution nucleotides online systems sequence alignment statistical models

MONKEYTool Content

http://labs.csb.utoronto.ca/moses/monkey.html [open in a new window]

Share This Link
Sequence Comparison > Analysis of Aligned Sequences

MONKEY is a set of programs designed to search alignments of non-coding DNA sequence for matches to matrices representing the sequence specificity of transcription factors.

links directory index: 132
TitlePublication YearGoogle Scholar Citation Count
MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model2004132
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsbinding sites biological evolution conserved sequence dna dna-binding proteins fungal dna gene expression regulation genetic models saccharomyces cerevisiae saccharomyces cerevisiae proteins sequence alignment species specificity transcription factors
setsUniversity of Toronto

MPI ToolkitTool Content

http://toolkit.tuebingen.mpg.de [open in a new window]

Share This Link
DNA > Phylogeny Reconstruction
Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Biochemical Features
Protein > Do-it-all Tools for Protein
Protein > Domains and Motifs
Protein > Phylogeny Reconstruction
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments
Sequence Comparison > Similarity Searching and Classification

Max-Planck Institute Bioinformatics Toolkit provides access to many different bioinformatics software tools and databases for sequence similarity searching, multiple sequence alignments, phylogenetic analysis, and protein structure prediction.

This content is being maintained by mremmert.

links directory index: 81
TitlePublication YearGoogle Scholar Citation Count
The MPI Bioinformatics Toolkit for protein sequence analysis200681
NAR Web Server Issue 2006
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagscomputational biology protein conformation protein sequence analysis proteins sequence alignment

MulanTool Content

http://mulan.dcode.org/ [open in a new window]

Share This Link
Sequence Comparison > Multiple Sequence Alignments

Mulan is a multiple sequence alignment tool. It employs novel algorithms such as TBA and multiTF to respectively perform alignments and discover transcription factor binding sites. Results can be viewed as dot-plots of individual sequence alignments, or dynamically browsed with the ability to zoom in from sequence conservation profiles down to the level of the individual characters of the sequence alignment.

links directory index: 146
TitlePublication YearGoogle Scholar Citation Count
Mulan: multiple-sequence local alignment and visualization for studying function and evolution2005146
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsanimals anura binding sites chickens computational biology conserved sequence dna-binding proteins fishes gata3 transcription factor genome human genome humans mice molecular evolution nucleic acid sequence homology phylogeny rats sequence alignment trans-activators

Multi-HarmonyTool Content

http://www.ibi.vu.nl/programs/shmrwww [open in a new window]

Share This Link
Protein > Sequence Comparison
Protein > Sequence Features
Sequence Comparison > Multiple Sequence Alignments

Multi-Harmony is an interactive web server for detecting sub-type specific sites in proteins starting from a multiple sequence alignment. Combines Sequence Harmony and Multi-Relief methods.

links directory index: 7
TitlePublication YearGoogle Scholar Citation Count
Multi-Harmony: detecting functional specificity from sequence alignment20107
NAR Web Server Issue 2010
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsalgorithms protein sequence analysis sequence alignment smad proteins

MultiPhylTool Content

http://www.cs.nuim.ie/distributed/multiphyl.php [open in a new window]

Share This Link
DNA > Phylogeny Reconstruction
Protein > Phylogeny Reconstruction
Sequence Comparison > Analysis of Aligned Sequences

MultiPhyl is a high-throughput Maximum Likelihood based phylogeny analysis program that allows researchers to create a virtual phylogenetic supercomputer from a group semi-idle desktop machines.

links directory index: 106
TitlePublication YearGoogle Scholar Citation Count
MultiPhyl: a high-throughput phylogenomics webserver using distributed computing200757
DPRml: distributed phylogeny reconstruction by maximum likelihood200549
NAR Web Server Issue 2007
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsalgorithms animals computational biology computer simulation computing methodologies dna sequence analysis genetic databases genetic models genomics humans likelihood functions molecular evolution phylogeny sequence alignment statistical models

Associated Tag Cloud