Bioinformatics and Functional Genomics 3rd Edition

Chapter 3 Links 3.1-3.10

This page offers the web documents that are referred to in Chapter 3 of the book, as well as various resources. In Chapter 3 we describe the pairwise alignment of two DNA or protein sequences. This is one of the most fundamental operations in bioinformatics. We discuss ways to assign scores to two aligned protein sequences. We also introduce ways to globally or locally align two sequences.

WebLink Site URL
3.1 TimeTree http://timetree.org
3.2 BLAST at NCBI http://www.ncbi.nlm.nih.gov/BLAST/
3.3 Gap penalties http://www.ncbi.nlm.nih.gov/blast/html/sub_matrix.html
3.4 ExPASy http://www.expasy.ch/sprot/relnotes/relstat.html
3.5 EMBOSS align http://www.ebi.ac.uk/emboss/align/
3.6 Galaxy http://usegalaxy.org
3.7 EMBOSS http://emboss.sourceforge.net/
3.8 FASTA http://fasta.bioch.virginia.edu/fasta_www2/fasta_list2.shtml
3.9 FASTA at EBI http://www.ebi.ac.uk/fasta33/
3.10 Dotlet http://myhits.isb-sib.ch/cgi-bin/dotlet