Datatypes: Know your Ingredients

A section dedicated to describing the most common datatypes: FASTA for sequence, PDB for structure, MSA and HMM modifications to FASTA, domain output, blast output, blast databases, annotation data, etc.

Function Prediction

How to get information associated with your sequence.

BLAST Hacks

An expose on the blast tool for sequence search, and a number of ways it can be used.




NCBI
wikipedia
WU-BLAST

Structure Prediction

A post on homology modelling, sequence similarity search, etc.

Phylogenetic Trees

A post about the construction and analysis of phylogenetic trees.




Neighbor Joining
Phyml

MSA: Multiple Sequence Alignment

A Post about multiple sequence alignment construction and analysis




http://en.wikipedia.org/wiki/Multiple_sequence_alignment

paper: 2007 recent evolution of multiple sequence alignment programs
http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1963500
http://compbiol.plosjournals.org/perlserv/?request=get-document&doi=10.1371%2Fjournal.pcbi.0030123&ct=1



T-Coffee Tree-based Consistency Objective Function For alignment Evaluation (progressive)
http://www.tcoffee.org/

Muscle multiple sequence alignment by log-expectation
http://www.drive5.com/muscle/

Clustalw
http://www.ebi.ac.uk/Tools/clustalw2/index.html

Mafft MSA algorithm based on fast Fourier. transform
http://align.bmr.kyushu-u.ac.jp/mafft/software/source.html

Show how to download and install each
Show how to run each

publish a little perl script that is able to compare the results of all four, for establishing consistency between the four: number of columns in agreement between the submitted msas

Introduction

Hello and welcome to Pragmatic Bioinformatics; a source of practical tool review, handy code, and general tips for budding and seasoned computational biologists alike.