Identification of Polymorphic Markers for Genetic Mapping - Genomics: Essential Methods - page 46

7. dbSNP http://www.ncbi.nlm.nih.gov/projects/SNP/ (last accessed May 2010). The NCBI database
of sequence variation. This is the central resource for searching databases of known SNPs and
indels.
8. WormBase http://www.wormbase.org/ (last accessed May 2010). This is a central community
resource for researchers that work with Caenorhabditis elegans and other nematodes. It serves as
the central repository for sequence variation, mutants, phenotypes and other information related
to nematode species.
9. FlyBase http://flybase.org/ (last accessed May 2010). This is the central community resource for
researchers that work with Drosophila melanogaster and other fly species. It contains extensive
information, including a database of known sequence variants, specific to fly model organisms.
10. UCSC http://genome.ucsc.edu/ (last accessed May 2010). The UCSC Genome Browser. This
widely used visualization tool makes it possible to browse genomes at any resolution (individual
bases to entire chromosomes), along with tracks showing annotated genes, conserved sequences,
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12. HapMap http://www.hapmap.org (last accessed May 2010). The website of the International
HapMap Project provides allele frequencies and genotype data for millions of SNPs characterized
in several human population.
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14. Cancer Genome Atlas Consortium (2008) Comprehensive genomic characterization defines human
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15. Primer3Plus http://www.bioinformatics.nl/cgi-bin/primer3plus/primer3plus.cgi (last accessed May
2010). This online tool for provides interactive, highly customizable design of PCR assays based
on the primer3 design algorithm.
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17. Phred http://www.phrap.org/phredphrap/phred.html (last accessed May 2010). This is the site for
downloading Phred , the widely used basecaller for capillary-based sequencing that provides a
numeric quality score for each base position.
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19. Polyphred http://droog.gs.washington.edu/polyphred (last accessed May 2010). This is the site for
downloading Polyphred , a suite of programs from the University of Washington for basecalling,
alignment, assembly and SNP/indel discovery in capillary-based sequencing data.
20. Phrap http://www.phrap.org (last accessed May 2010). This is the site for downloading Phrap ,a
widely used assembly program, and cross_match, a sequence alignment algorithm.
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