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Links tagged with 'molecular evolution'

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Found 59 links

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Berkeley Phylogenomics GroupTool Content

http://phylogenomics.berkeley.edu/

DNA > Phylogeny Reconstruction
Protein > 3-D Structure Prediction
Protein > Domains and Motifs
Protein > Phylogeny Reconstruction
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Comparative Genomics
Sequence Comparison > Multiple Sequence Alignments

The Berkeley Phylogenomics Group provides a series of web servers for phylogenomic analysis: classification of sequences to pre-computed families and subfamilies using the PhyloFacts Phylogenomic Encyclopedia, FlowerPower clustering of proteins sharing the same domain architecture, MUSCLE multiple sequence alignment, SATCHMO simultaneous alignment and tree construction, and SCI-PHY subfamily identification.

NAR Web Server Issue 2007
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tagsalgorithms amino acid motifs amino acid sequence amino acid sequence homology animals artificial intelligence bayes theorem binding sites computational biology gene expression profiling genetic databases genetic models humans likelihood functions markov chains molecular evolution molecular sequence data phylogeny protein conformation protein databases protein sequence analysis proteins reproducibility of results sensitivity and specificity sequence alignment src homology domains statistical models tertiary protein structure time factors

CAMPOTool Content

http://schubert.bio.uniroma1.it/CAMPO/index.html

Sequence Comparison > Analysis of Aligned Sequences

CAMPO is a tool to analyze conserved regions from a multiple sequence alignment

NAR Web Server Issue 2005
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tagscomputational biology hydrophobic and hydrophilic interactions molecular evolution molecular models potassium channels protein conformation proteins trypsin inhibitors

CHC_FINDTool Content

http://schubert.bio.uniroma1.it/CHC_FIND/index.html

Protein > 3-D Structural Features
Protein > 3-D Structure Comparison
Sequence Comparison > Analysis of Aligned Sequences

CHC_FIND is a tool to analyze conserved hydrophobic contacts (CHC) from multiple structural alignments. In addition to a multiple sequence alignment, a structural alignment which provides the superposition of structurally conserved regions (SCRs) (i.e., results from SCR_FIND) needs to be provided.

NAR Web Server Issue 2005
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tagscomputational biology hydrophobic and hydrophilic interactions molecular evolution molecular models potassium channels protein conformation proteins trypsin inhibitors

COGsTool Content

http://www.ncbi.nlm.nih.gov/COG/

Protein > Domains and Motifs
Sequence Comparison > Comparative Genomics

Clusters of Orthologous Groups represent ancient conserved protein domains; use COGnitor tool to find COGS in sequence of interest.

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tagsamino acid sequence animals archaea archaeal genes archaeal proteins bacteria bacterial genes bacterial proteins caenorhabditis elegans conserved sequence drosophila melanogaster factual databases fungal genes fungal proteins genome methanococcus molecular evolution multigene family phylogeny proteins saccharomyces cerevisiae sequence alignment species specificity

COMPASSTool Content

http://prodata.swmed.edu/compass/compass.php

Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Similarity Searching

COMPASS (Comparison of Multiple Protein Alignments with Assessment of Statistical Significance) is a tool for detecting remote levels of sequence similarity using profile-based comparison of multiple sequence alignments. Statistics and speed have been improved, and visualization tools introduced.

NAR Web Server Issue 2007NAR Web Server Issue 2009
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tagsamino acid motifs amino acid sequence amino acid sequence homology capsid proteins clathrin computational biology mamastrovirus molecular evolution molecular models molecular sequence data protein conformation protein databases protein structural homology proteins reproducibility of results secondary protein structure sensitivity and specificity sequence alignment statistical data interpretation statistics as topic tertiary protein structure trna methyltransferases

ConPlexTool Content

http://sbi.postech.ac.kr/ConPlex/

Protein > 3-D Structure Comparison

ConPlex is a web server that enables conservation analyses of protein interactions within protein quaternary structures. Results of the residue specific conservation analysis are displayed on the input protein complex structure.

NAR Web Server Issue 2010
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tagsamino acid sequence homology molecular evolution multiprotein complexes quaternary protein structure

ConSurfTool Content

http://consurf.tau.ac.il/

Protein > 3-D Structural Features
Sequence Comparison > Analysis of Aligned Sequences

The ConSurf server allows one to map levels of amino acid conservation to known protein structures in order to study areas of potential functional importance on the surface of the protein. A PDB file is required as input, and a multiple sequence alignment is optional. If an alignment is not provided, ConSurf will build one by performing a search for homologous sequences and then aligning them. ConSurf 2010 combines ConSurf and ConSeq for an easier, more intuitive interface.

NAR Web Server Issue 2005NAR Web Server Issue 2010
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tagsamino acid sequence amino acid sequence homology amino acid substitution amino acids bacterial proteins base sequence bayes theorem bcl-x protein conserved sequence molecular evolution molecular models nucleic acid conformation phylogeny potassium channels protein conformation protein databases protein sequence analysis proteins proto-oncogene proteins c-bcl-2 sequence alignment sequence analysis

DCODE.ORGResource Content

http://www.dcode.org/

Human Genome > Other Resources
Sequence Comparison > Comparative Genomics

The dcode.org website provides access to tools for comparative genomic analyses developed by the Comparative Genomics Center at the Lawerence Livermore National Laboratory. Tools include: zPicture, Mulan, eShadow, rVista, CREME, and the ECR Browser.

NAR Web Server Issue 2005
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tagsbase sequence binding sites computational biology gene expression regulation genetic promoter regions genomics humans molecular evolution nucleic acid regulatory sequences phylogeny sequence alignment transcription factors

DISULFINDTool Content

http://disulfind.dsi.unifi.it/

Protein > Biochemical Features
Protein > Sequence Features

DISULFIND is a server for predicting the disulfide bonding state of cysteines and their disulfide connectivity given a protein sequence.

This content is being maintained by paolo.frasconi.

NAR Web Server Issue 2006
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tagsalgorithms amino acid sequence artificial intelligence binding sites computational biology computer simulation cysteine disulfide bridges disulfides gene expression profiling histidine machine learning metalloproteins molecular evolution molecular sequence data neural networks (computer) protein binding protein databases protein sequence analysis proteins sequence alignment

ET Report MakerTool Content

http://mammoth.bcm.tmc.edu/report_maker/

Protein > 3-D Structural Features
Protein > Annotation and Function

Evolutionary trace (ET) report maker pools information from different sources including databases and on-the-fly multiple sequence analysis to produce a pdf formatted document as output. The emphasis is on prediction of functional sites of proteins.

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tagsalgorithms animals biological evolution computational biology humans molecular evolution mutation protein databases proteins statistical models

fastSCOPTool Content

http://gemdock.life.nctu.edu.tw/fastSCOP/

Protein > 3-D Structure Comparison
Protein > Domains and Motifs
Sequence Comparison > Similarity Searching

fastSCOP identifies structural domains and determines evolutionary superfamilies of a query protein structure using 3D-BLAST to scan SCOP and MAMMOTH to create a structural alignment for refining domain boundaries.

NAR Web Server Issue 2007
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tagsamino acid sequence amino acid sequence homology computational biology molecular evolution molecular models molecular sequence data protein conformation protein databases protein sequence analysis protein structural homology proteins statistical data interpretation tertiary protein structure

FGFTool Content

http://fgf.genomics.org.cn/service/index.jsp

Protein > Phylogeny Reconstruction
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching

FGF (Fishing Gene Family) is a resource for finding gene families given a set of protein sequences by investigating phylogenetic trees, duplication fate, and selective pressure (ka/ks calculations).

NAR Web Server Issue 2007
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tagsalgorithms animals chromosome mapping chromosomes computational biology gene duplication genetic models genome humans molecular evolution phylogeny

GenDecoderTool Content

http://darwin.uvigo.es/software/gendecoder.html

DNA > Structure and Sequence Feature Detection
Sequence Comparison > Multiple Sequence Alignments

GenDecoder is a prediction server for animal mitochondrial genetic codes. It provides information about codon-usage, amino acid composition, GC content and a final genetic code prediction for a mitochondrial genome sequence.

NAR Web Server Issue 2006
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tagsamino acid sequence animals base sequence codon conserved sequence mitochondrial genes molecular evolution protein biosynthesis sequence alignment sequence analysis

GeneFizzTool Content

http://pbga.pasteur.fr/GeneFizz/

DNA > Gene Prediction

GeneFizz is a tool for identifying genes using by using the physical characteristics of helix-to-coil transitions in DNA.

NAR Web Server Issue 2003
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tagsalgorithms animals biophysical phenomena biophysics computational biology dna dna sequence analysis drosophila melanogaster genes genetic code genetic models genetic techniques genomics molecular evolution nucleic acid conformation plasmodium falciparum protozoan dna protozoan genes protozoan genome

GLUE, GLUE-IT, PEDEL, PEDEL-AA and DRIVeRTool Content

http://guinevere.otago.ac.nz/stats.html

DNA > Tools For the Bench

GLUE, PEDEL, and DRIVeR are tools for estimating completeness and diversity in randomized protein-encoding libraries; useful for guiding library design and for analyzing results. GLUE Including Translation (GLUE-IT) finds the expected amino acid completeness of libraries. PEDEL-AA calculates amino acid statistics for libraries generated by epPCR.

NAR Web Server Issue 2008
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tagsalgorithms chemical models codon computer simulation directed molecular evolution dna dna mutational analysis dna sequence analysis gene library genetic models genetic variation molecular evolution mutagenesis mutation peptide library point mutation polymerase chain reaction protein sequence analysis proteins statistical models