Showing posts with label BLAST. Show all posts
Showing posts with label BLAST. Show all posts

Monday, March 28, 2011

Workshop on Molecular Evolution: North America, 24 July - 6 August 2011


The Workshop on Molecular Evolution consists of a series of lectures, demonstrations and computer laboratories that cover various aspects of molecular evolution. Demonstrations and consultations on the use of computer programs and packages such as BLAST, BEAST, Clustal W and Clustal X, FASTA, FigTree, GARLI, Genealogical Sorting Index, LAMARC, MAFFT, Migrate-n, MrBayes, PAML, PAUP*, and SeaView will be provided. The course is designed for established investigators, postdoctoral scholars, and advanced graduate students with prior experience in molecular evolution and related fields. Admission is limited and highly competitive, with admissions decisions determined by an international committee.

Topics to be covered include:
  • Databases and sequence matching: database searching: protein sequence versus protein structure; homology; mathematical, statistical, and theoretical aspects of sequence database searches
  • Phylogenetic analysis: theoretical, mathematical and statistical bases; sampling properties of sequence data; Bayesian analysis; hypothesis testing
  • Maximum likelihood theory and practice in phylogenetics and population genetics: coalescent theory; maximum likelihood estimation of population genetic parameters
  • Molecular evolution integrated at organism and higher levels: population biology; biogeography; ecology; systematics and conservation
  • Molecular evolution and development: gene duplication and divergence; gene family organization; coordinated expression in evolution
  • Comparative genomics: genome content; genome structure; genome evolution
  • Molecular evolution integrated at lower levels: biochemistry; cell biology; physiology; relationship of genotype to phenotype

Venue: Colorado State University, Fort Collins, Colorado, USA
Application form and complete schedule are available online.

Thursday, March 24, 2011

cBARBEL: Catfish Breader And Researcher Bioinformatics Entry Location

cBARBEL is an online open-access database for genome biology of Ictalurus spp.. It is a comprehensive, integrative platform for all aspects of catfish genetics, genomics and related data resources. cBARBEL provides BLAST-based, fuzzy and specific search functions, visualization of catfish linkage, physical and integrated maps, a catfish EST contig viewer with SNP information overlay, and GBrowse-based organization of catfish genomic data based on sequence similarity with zebrafish chromosomes. 

cBARBEL provides links to simple daily-use informatics tools that database users may need while accessing cBARBEL, including the external NCBI BLAST server, SMART domain search, ClustalW-based multiple sequence alignments and basic nucleotide to amino acid translation. These tools are provided in-frame so that the user does not need to leave the cBARBEL site for small-scale sequence analysis. Publications relevant to catfish genomics and genetics are also linked. Additionally, the recently created Teleost Alternative Splicing Database (TASD) with alternative splicing data for catfish ESTs is linked to cBARBEL.