traminer.unige.ch
TraMineR
http://traminer.unige.ch/documentation.shtml
Who uses it ]. Help and contact ]. You can see here a short preview. Of what TraMineR can do for you. Just have a look to get the flavour of TraMineR's main features and of how easy it is to put them at work. Reference manual [html] , [pdf] . See also the TraMineR page on the CRAN . The User's guide of TraMineR. Pdf, 3.6MB) describes the features and usage of TraMineR by means of many examples from the social sciences. It may also serve as an introduction to discrete sequential data analysis. Suffix tree...
big.crg.cat
Comparative Bioinformatics | Bioinformatics and Genomics @ CRG
http://big.crg.cat/comparative_bioinformatics
MotEvo: integrated Bayesian probabilistic methods for inferring regulatory sites and motifs on multiple alignments of DNA sequences. AMPA: an automated web server for prediction of protein antimicrobial regions. Use of ChIP-Seq data for the design of a multiple promoter-alignment method. Accurate multiple sequence alignment of transmembrane proteins with PSI-Coffee. Transcription Factor Binding Site Positioning in Yeast: Proximal Promoter Motifs Characterize TATA-Less Promoters.
snf2.net
Snf2 Family Protein Resource - links
http://www.snf2.net/snf2/links.shtml
Original SNF2 family album. Supporting Eisen et al. Search and multiple alignment. Please don't hesitate to send us. Any suggestions or corrections. Snf2net is maintained at National University of Ireland Galway and University of Dundee, Scotland.
birgiuse.blogspot.com
BiRG Lab Blog: July 2008
http://birgiuse.blogspot.com/2008_07_01_archive.html
Indiana University Southeast BioInformatics Research Group Web Log. Friday, July 25, 2008. Get the basics about dot plots. Know how to interpret the most common patterns in a dot plot. Use Lalign to extract local alignments. Database searches are useful for finding homologues. Database searches don't provide precise comparisons. More precise tools are needed to analyze the sequences in detail including. Dot plots for graphic analysis. Local or global alignments for residue/residue analysis. Dotlet is one...
slackalaxy.wordpress.com
Biology and Slackware | slackalaxy
https://slackalaxy.wordpress.com/sbio
This is a list of biology and chemistry oriented software, available at SlackBuilds.org. Links are to the web-sites of the corresponding software. You will find hundreds of programs covering areas such as sequence alignment, database searching, protein motif identification, nucleotide sequence pattern analysis, codon usage analysis, rapid identification of sequence patterns, presentation tools for publication. Main scope of Arka is the manipulation and visualisation of DNA / RNA / protein sequences.
big.crg.es
Comparative Bioinformatics | Bioinformatics and Genomics @ CRG
http://big.crg.es/comparative_bioinformatics
MotEvo: integrated Bayesian probabilistic methods for inferring regulatory sites and motifs on multiple alignments of DNA sequences. Accurate multiple sequence alignment of transmembrane proteins with PSI-Coffee. AMPA: an automated web server for prediction of protein antimicrobial regions. Use of ChIP-Seq data for the design of a multiple promoter-alignment method. Transcription Factor Binding Site Positioning in Yeast: Proximal Promoter Motifs Characterize TATA-Less Promoters.
selectome.unil.ch
Methods - Selectome
http://selectome.unil.ch/cgi-bin/methods.cgi
Selectome: a Database of Positive Selection. CodeML is a program from the package PAML. It estimates various parameters (Ts/Tv, dN/dS, branch length) on the codon (nucleotide) alignment, according to the phylogenetic tree. The parameter of interest to us is ω = dN/dS. Which indicates selective pressure. Selectome uses the branch-site model. Which estimates different dN/dS values among branches and among sites. A branch of interest is selected and called ". 34; All other branches in the tree are the ".
SOCIAL ENGAGEMENT