Bioinformatic Resources

This page looks at

• General Information
• Bioinformatic Tools
• Miscellaenous Bioinformatic Links

Introduction

Bioinformatics is, at its simplest level, using computers to analyse the genetic sequence of organisms. It allows us to make sense of the incredibly large volumes of sequence information being generated by projects such as HUGO (The Human Genome Project) and Celera (commercial effort at sequencing the entire human genome) as well as many others. Links to general information sites.

• BLAST(Basic Local Alignment Search Tool)
  BLAST stands for Basic Local Alignment Search Tool and is a program to locate regions of sequence similarity with a view to comparing structure and function.
  
• FASTA
  Like BLAST, the FASTA3 program is used in order to carry out the homological comparison of a given sequence to the sequences in the nucleotide and amino acid databases worldwide however it uses a different algorithm.
• SRS
  SRS allows the querying and retireval of sequences from sequence databases.
• CLUSTALW
  CLUSTALW determines the optimal alignment of a set of nucleotide or amino acid sequences.
• Genedoc
  Genedoc allows one to visualise alignments such as those generated by CLUSTALW.
• BioEdit
  Initially designed as a standalone alignment viewer BioEdit is useful for calculating potential AA content and mass. It is capable of interconversion between different file formats from a mainframe computer.
• Phylip
  This package allows one to visualise the evolutionary relatedness of sequences.
• Treeview
  This package allows one to visualise the evolutionary relatedness of sequences.
  Blocks Searcher
  Blocks Searcher is a homology searching system that is based on a database of protein family representations rather than sequences.
• Motif Searcher
  Motif Searcher allows one to look for contiguous stretches of amino acids (called motifs) shared by a group of proteins and conserved for function.
• OrfFinder
  Orfinder identifies all possible ORFs in a DNA sequence by locating the stop and start codons.
• Swiss Model
  The Swiss Model server attempts to predict the 3D structure of a protein from its amino acid sequence.
• Protparam
  This is a collection of algorithms that facilitate the prediction of physiochemical properties on a given amino acid sequence.
• PSort
  PSORT is a computer program for the prediction of protein localization sites in cells.
• ReadSeq
  ReadSeq simply and efficiently interconverts between different formats.
• Predict Protein
  PredictProtein is a service for sequence analysis, and structure prediction.
  
• SignalP
  SignalP looks for signal sequences within a given sequence.
• Genemark
  Genemark attempts to locate and identify potential genes in a given sequence.
• Genefinder
  Genefinder also attempts to locate and identify potential genes in a given sequence.

• Dictionary of Cell and Molecular Biology
• Medline
  
  Medline contains a wealth of bioinformatic and medical articles.
  

  ---

  
  
  

  Declan McGrath, BSc.
  IT Department
  NUI Galway
  
  Email: declan.mcgrath@geminga.it.nuigalway.ie
  
  Date Last Updated: 29th June 2001