Description

BLAST

Sequence similarity searching.

ClustalW

Multiple sequence alignment.

ClustalX

Graphical user interface for ClustalW..

Ingenuity Pathway Analysis

Molecular pathway prediction.

Gibbs

Detection of multiple conserved regions within DNA or protein sequences.

GBrowse

Visualization of genomic sequence and sequence features.

Lasergene

Sequence analysis (alignment, motif finding, phylogenetic analysis)

MEME/MAST

Motif detection using expectation/maximization algorithms.  Database searching for motifs.

MUSCLE

Multiple sequence alignment.

Partigene

EST data analysis

PAUP

Phylogenetic analysis.

Phrap

Base calling, sequence comparisons and sequence assembly.

Phred

Processes DNA sequencing trace files, calls bases and assigns a quality value to each called base.

PHYLIP

Phylogenetic analysis.

PipMaker

Genomic sequence alignment.

R

Statistical computing.

RepeatMasker

Identification of interspersed repeats and low complexity DNA.

Sequencher

Sequence assembly.

Taverna

Facilitates analysis workflows and distributed compute technology.

T-coffee

Multiple sequence alignment.

TimeLogic DeCypher

Hardware accelerated sequence analysis (BLAST, HMM, and SW)

Trace2dbest

Processes EST sequence traces.

TRANSFAC

Regulatory motif discovery tool.

TreeView

Phylogenetic tree display and editing.

Vector NTI Suite

Sequence analysis (alignment, motif finding, phylogenetic analysis)

Weeder

Transcription factor binding site identification in co-regulated genes.

Description

BLAST

Sequence similarity searching.

ClustalW

Multiple sequence alignment.

ClustalX

Graphical user interface for ClustalW..

Ingenuity Pathway Analysis

Molecular pathway prediction.

Gibbs

Detection of multiple conserved regions within DNA or protein sequences.

GBrowse

Visualization of genomic sequence and sequence features.

Lasergene

Sequence analysis (alignment, motif finding, phylogenetic analysis)

MEME/MAST

Motif detection using expectation/maximization algorithms.  Database searching for motifs.

MUSCLE

Multiple sequence alignment.

Partigene

EST data analysis

PAUP

Phylogenetic analysis.

Phrap

Base calling, sequence comparisons and sequence assembly.

Phred

Processes DNA sequencing trace files, calls bases and assigns a quality value to each called base.

PHYLIP

Phylogenetic analysis.

PipMaker

Genomic sequence alignment.

R

Statistical computing.

RepeatMasker

Identification of interspersed repeats and low complexity DNA.

Sequencher

Sequence assembly.

Taverna

Facilitates analysis workflows and distributed compute technology.

T-coffee

Multiple sequence alignment.

TimeLogic DeCypher

Hardware accelerated sequence analysis (BLAST, HMM, and SW)

Trace2dbest

Processes EST sequence traces.

TRANSFAC

Regulatory motif discovery tool.

TreeView

Phylogenetic tree display and editing.

Vector NTI Suite

Sequence analysis (alignment, motif finding, phylogenetic analysis)

Weeder

Transcription factor binding site identification in co-regulated genes.

Tool

Description

Basic Local Alignment Search Tool [BLAST]

A sequence similarity search program (NCBI).

VISTA [VISTA]

A suite of programs and databases for comparative analysis of genomic sequences.

Z-Picture [ZPicture]  

A dynamic alignment and visualization tool that is based on the blastz alignment program used by PipMaker.

Multi/PipMaker [Pipmaker]

A tool to computes alignments of similar regions in two DNA sequences.

UCSC Genome Browser [UCSC]

A tool to visualize and explore cross-species genomic sequences.

Ensembl Genome Browser [Ensembl]

A tool to visualize and explore cross-species genomic sequences.

RepeatMasker [RepeatMasker]

A tool to screen DNA sequences in FASTA format against a library of repetitive elements and returns a masked query sequence ready for database searches.

TRANSFAC [TRANSFAC]

A database of eukaryotic transcription factors, their genomic binding sites and DNA-binding profiles.

DDBJ/EMBL/GenBank® [DDBJ] [EMBL] [GenBank]

Mirror database repositories for nucleotide sequences.

Ensembl [Ensembl]

A resource for annotated eukaryotic genomes.

NCBI Gene [NCBI Gene]

A gateway that integrates information from LocusLink and from genes annotated on Reference Sequences from completely sequenced genomes.

NCBI GenPept [GenPept]

A database of automated translations of GenBank® nucleotide sequences.

NCBI Reference Sequences [RefSeq]

NCBI Reference Sequences.

TIGR Gene Indices [TIGR Gene Indices]

EST clusters for diverse species.

UniGene [UniGene]

An experimental system that automatically partitions GenBank® sequences into non-redundant sets of gene-oriented clusters.

UniProt [UniProt]

UniProt (Universal Protein Resource) is a comprehensive catalogue of information on proteins. It is a central repository of protein sequence and function created by joining the information contained in UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and PIR.

InterPro [InterPro]

A database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to unknown protein sequences.

PROSITE [PROSITE]

A database of protein families and domains consisting of biologically significant sites, patterns and profiles that help to reliably identify to which known protein family a new sequence belongs.

Protein Data Bank [PDB]

A repository for processing and distribution of 3-D biological macromolecular structure data.

Protein Domain Families [ProDom]

A comprehensive set of protein domain families automatically generated from the SWISS-PROT and TrEMBL sequence databases.

Protein Families Database of Alignments and HMMs [Pfam]

A large collection of multiple sequence alignments and hidden Markov models covering common protein domains and families.

Protein Fingerprints [PRINTS]

A compendium of protein fingerprints or groups of conserved motifs used to characterize a protein family.

Simple Modular Architecture Research Tool [SMART]

A resource that allows the identification and annotation of genetically mobile domains and the analysis of domain architectures.

Biomolecular Interaction Network Database (BIND)

A resource for curated protein-protein interactions.

Database of Interacting Proteins (DIP)

A catalog of experimentally determined interactions between proteins.

Comparative Toxicogenomics Database [CTD] 

A resource to enhance understanding about the effects of environmental chemicals on human health.

Environment, Drugs and Gene Expression [EDGE]

A scientific resource for toxicology-related gene expression information.

NLM® Toxicogenomics [Toxicogenomics]

A compendium of Internet resources related to toxicogenomics.

ArkDB [ArkDB]

A comprehensive public repository for genome mapping data from farmed and other animal species.

Ciona intestinalis [Ciona intestinalis]

DOE Joint Genome Institute Ciona intestinalis genome project.

FlyBase [FlyBase]

Database of the Drosophila Genome.

Fugu Genome Project [Fugu Genome Project]

Provides access to the whole-genome sequence of the Fugu.

The Fugu Genomics Project [The Fugu Genomics Project]

Access to resources geared towards understanding sequence data generated by the human genome project by studying the Fugu ribripes genome.

Genomic Research on Atlantic Salmon Project [GRASP]

A project that aims to coordinate all aspects of genomics research on Atlantic salmon.

Medakafish Homepage [Medakafish Homepage]

A database for the medaka model organism.

Mouse Genome Informatics [MGI]

A resource that provides integrated access to data on the genetics, genomics and biology of the laboratory mouse.

Online Mendelian Inheritance in Man [OMIM]

A catalog of human genes and genetic disorders.

Rat Genome Database [RGD]

A resource that curates and integrates rat genetic and genomic data and provides access to this data to support research using the rat as a genetic model for the study of human disease.

Xiphophorus [Xiphophorus]

A resource dedicated to the Poeciliid fish genus Xiphophorus.

The Zebrafish Information Network [ZFIN]

The zebrafish model organism database.

Gene Ontology Consortium [GO]

A collaborative effort to provide structured vocabularies that describe gene products consistently across organisms and databases.

HomoloGene [HomoloGene]

A resource of curated and calculated orthologs for genes as represented by UniGene or by annotation of genomic sequences.

Homologous Vertebrate Genes Database [HOVERGEN]

A database of homologous vertebrate genes allowing visualization of multiple alignments and phylogenetic trees.

National Center for Biotechnology Information [NCBI]

A US national resource for molecular biology information.

NCBI Taxonomy [NCBI Taxonomy]

The taxonomy of organisms represented in NCBI sequence databases.

Course Title

Dates

Description

Attendees

A Field Guide to GenBank and NCBI Molecular Biology Resources

June 2005;
March 2006

A workshop designed to instruct attendees about the biomedical resources available at the National Library of Medicine’s National Center for Biotechnology Information (NCBI)
Instructor: NCBI staff
Location: The Jackson Laboratory

Undergraduate and High School Students, Postdoctoral Fellows and Faculty

Unix

July 2005

A workshop to introduce the UNIX command line environment with an emphasis on using popular computational biology tools such as BLAST, BLAT, and the Gibbs Sampler.
Instructor: Dr. Joel Graber, The Jackson Laboratory
Location: MDIBL

Undergraduate and High School Students, Postdoctoral Fellows and Faculty

Introduction to Perl Programming for Bioinformatics

August 2005

A workshop designed to teach attendees to:  write and run Perl programs; understand Perl syntax and scoping; read and write files; understand Perl's data types and how to use complex data structures; handle errors; generate messages and terminate gracefully; use various built-in functions; write loops, branches, and related control structures; process text; use regular expressions; process command-line arguments; and write clean, maintainable, modular code (comments, subroutines, etc.)
Instructor: Sean Quinlan, Boston University
Location: MDIBL

Undergraduate and High School Students, Postdoctoral Fellows and Faculty

Practical Genomics and Bioinformatics

May 2004; May 2006

An intensive introduction to experimental procedures in the analysis of gene sequences and gene expression, including RNA isolation, reverse trancription, polymerase chain reaction, direct sequencing, and real time quantitative PCR. The theoretical basis of each technique will be presented in sufficient depth for understanding its application. Students will be asked to work as a coordinated team to address an open-ended original question that may result in new sequence data to be submitted to the Gen Bank database.
Instructors: Dr. T. Glen Lawson, Bates College; Dr. David Towle, MDIBL
Location: MDIBL

Bates College undergraduates

Molecular Biology Research Techniques

May 2002; March 2003; November 2004;
May 2005; March 2006; April 2006

An intensive introduction to experimental procedures in the analysis of gene sequences and gene expression, including RNA isolation, reverse transcription, polymerase chain reaction, direct sequencing, and real-time quantitative PCR.
Instructor: Dr. David Towle, MDIBL
Location: MDIBL

Undergraduates from University of Maine - Farmington, University of Maine - Machias, College of the Atlantic, and Bates College

Functional Genomics of Membrane Transport

March 2003;  March 2006;
March 2007;
March 2008

The course will focus on cystic fibrosis as a model disease that can be studied with a variety of techniques currently used in biomedical research, and it will consist of both lectures and hands-on training in the laboratory. Students will identify CFTR sequences and use bioinformatics and computational techniques to compare sequences.
Instructors: Dr. Denry Sato, MDIBL; Dr. Bruce Stanton, Dartmouth Medical School
Location: MDIBL

UMaine Honors College Undergraduates

Environmental Toxicogenomics