Computational biology

From Shiu Lab

Contents 1 Package of comp biol software 2 Resource links 3 Journals 4 Python 5 Gene finding 6 Assembly 7 Sequence visualization and editing 8 Pairwise alignment 9 Multiple sequence alignemnt 10 Motif finding 11 Clustering 12 Structural prediction 13 Statistics 14 Microarray analysis 14.1 Tiling array 15 Transcription factor binding site 16 Molecular Evolution 16.1 Software packages 16.2 Tree reconciliation 16.3 Ancestral state inference 16.4 Sequence simulation 16.5 Divergence time 17 Population genetics 18 Systems biology 19 Database

Package of comp biol software

• EMBOSS

Resource links

• A long list of bioinformatic resources from Anil Jegga, Cincinnati Children's Hospital Medical Center

Journals

• A comprehensive list from Glasglow.

Python

• Biopython:installation note.
• Numeric

Gene finding

• Genefinding.org: a very comprehensive collection of resources.
• Genewise
• Augustus
• Glimmer
• GlimmerM
• Genscan
• GrailEXP

Assembly

• MUMMER
• AMOS
• Shorty: for short sequence assembly.
• Arachne
• PCAP

Sequence visualization and editing

• VisCoSe: Visualization and Comparison of Consensus Sequences

Pairwise alignment

• NCBI BLAST
• mpiBLAST: Parallelization of NCBI BLAST.

Multiple sequence alignemnt

• MAFFT
• MUSCLE
• ClustalW

Motif finding

• AlignACE
• MEME: download section and installation instruction.
• MDscan
• HMMER
• InterProScan
• Weeder
• MotifSampler
• YMF

Clustering

• Markov clustering
• Blastclust: included in the BLAST package
• FuzzyK

Structural prediction

• PredictProtein
• SwissModel: web interface, no local version.
• msuprotein:many useful links for protein structure prediction.

Statistics

• R: The R Project for Statistical Computing
• Bioconductor: an open source and open development software project for the analysis and comprehension of genomic data.
• BioC course: Very extensive tutorials on Bioconductor functionalities, from the Short Course ran at Bressanone, Italy in 2004
• R/BioC manual: From Thomas Girke, UC Riverside.

Microarray analysis

Tiling array

• Affymetrix tiling array tools: Integrated Genome Browser and Tiling Analysis Software from Affy.
• tilingArray: a Bioconductor package. Contain several functions available for finding segmentation patterns. Applied to a recently published paper.
• snapCGH: a Bioconductor package. The BioHMM module uses HMM to find segmentation patterns in CGH experiments, see the paper.

Transcription factor binding site

• TFBSfinder
• BioProspector
• BioOptimizer

Molecular Evolution

Software packages

• Phylip
• TNT
• PAML
• IDEA: Graphical user interface for some commonly used software such as PAML and PHYLIP.

Tree reconciliation

• Notung

Ancestral state inference

• Mesquite

Sequence simulation

• EvolveAGene: by Barry Hall

Divergence time

• TimeTree

Population genetics

• modeler4simcoal2: a modeler for coalescent processes

Systems biology

• Cytoscape: an open source bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data.
• GenMAPP: a free computer application designed to visualize gene expression and other genomic data on maps representing biological pathways and groupings of genes
• geWorkbench: genomics Workbench is a Java-based open-source platform for integrated genomics.
• Systems Biology Workbench: a software framework that allows heterogeneous application components-written in diverse programming languages and running on different platforms-to communicate and use each others' capabilities via a fast binary encoded-message system
• E-Cell: an object-oriented software suite for modeling, simulation, and analysis of large scale complex systems, particularly focused on biological details of cellular behavior.

Database

• BioCyc: a collection of 371 Pathway/Genome Databases
• KEGG BRITE: a collection of hierarchical classifications representing our knowledge on various aspects of biological systems