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Protocols
- A Guide to Molecular Sequence Analysis (Andrew S. Louka , www.SequenceAnalysis.com)
This guide will introduce the reader to molecular sequence analysis. In the context of this guide, sequence analysis is the process of trying to find out something about a nucleotide or amino acid sequence, employing in silico biology techniques. You may have sequenced a gene yourself, and wish to learn what the long string of letters representing bases, actually code for. You may want to confirm that you have indeed cloned a gene successfully, or you might want to learn about a sequence of DNA that you know absolutely nothing about. You may want to know if a worm has a similar protein to a human one. These, and many other situations, require that you employ sequence analysis.
http://www.sequenceanalysis.com/
Added: Fri Sep 27 2002, Hits: 4460, Reviews: 0
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Flexible Sequence Similarity Searching with the FASTA3 Program Package
(Humana Press )
provides a “hands on” overview of the programs in the FASTA
package. Rather than discuss
in depth the theory and practice of protein and DNA sequence comparison, this protocol
focus on more practical questions, such as: “Which FASTA program should
I use?”, “What threshold should I use for statistical significance?”, “Which
databases should I search?”, “When should I use FASTA and when should I use
BLAST?”, and “When should I change the scoring matrix and gap penalties?”
http://www.humanapress.com/pdfs/ch10185-.pdf
Added: Sun Jul 21 2002, Hits: 1320, Reviews: 0
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Protein sequence analysis - A practical guide
(Terri Attwood and Alex Michie )
This is an interactive exercise that aims to provide a taste of bioinformatics resources around the world by introducing a range of widely-used analysis tools and databases.
http://www.biochem.ucl.ac.uk/bsm/dbbrowser/jj/pref...
Added: Sat Sep 28 2002, Hits: 2759, Reviews: 0
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Yass
(Team Yass (laboratory LORIA in france))
YASS is a program to perform a local alignment of DNA sequences (fasta or plain format). Like most of heuristic local alignment algorithms (BLAST, FASTA, PATTERNHUNTER ...)
http://www.loria.fr/projets/YASS/
Added: Fri Apr 22 2005, Hits: 561, Reviews: 0
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