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DNA sequence analysis

DNA sequence analysis. Xu Cheng. DNA sequence analysis. Retrieving DNA sequences from databases Computing nucleotide compositions Identifying restriction sites Designing polymerase chain-reaction (PCR) primers Identifying open reading frames (ORFs)

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DNA sequence analysis

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  1. DNA sequence analysis Xu Cheng

  2. DNA sequence analysis • Retrieving DNA sequences from databases • Computing nucleotide compositions • Identifying restriction sites • Designing polymerase chain-reaction (PCR) primers • Identifying open reading frames (ORFs) • Predicting elements of DNA/RNA secondary structure • Finding repeats • Computing the optimal alignment between two or more DNA sequences • Finding polymorphic sites in genes (single nucleotide polymorphisms,SNPs) • Assembling sequence fragments

  3. Sequence quality control • Multiple reads on both DNA strands • Removing vector sequences • Repeat mask

  4. http://www.ncbi.nlm.nih.gov/VecScreen/VecScreen.html

  5. test • gi|4099437 • What’s the vector contamination?

  6. Computing/Verifying a Restriction Map • REBASE http://rebase.neb.com/rebase/rebase.html NEBcutter V2.0http://tools.neb.com/NEBcutter2/index.php • Webcutter 2.0 http://www.firstmarket.com/cutter/cut2.html • Restriction Maps http://arbl.cvmbs.colostate.edu/molkit/mapper/index.html • Just-bio cutter http://www.justbio.com/cutter/index.php

  7. Designing PCR Primers • Primer3 http://frodo.wi.mit.edu/ • Primer-Blast http://www.ncbi.nlm.nih.gov/tools/primer-blast/index.cgi?LINK_LOC=BlastHome

  8. Analyzing DNA Composition • G+C content • Counting words in DNA sequences • Counting long words in DNA sequences • Finding internal repeats in your sequence Dotplot:arbl.cvmbs.colostate.edu/molkit/ • Identifying genome-specific repeats in your sequence (NT_004559.13 )http://www.girinst.org/censor/index.php

  9. Finding Protein-Coding Regions • ORF Finder at NCBI (AE008569 )http://www.ncbi.nlm.nih.gov/gorf/gorf.html

  10. Analyzing your DNA sequencewith GeneMark • exon.gatech.edu/GeneMark/

  11. Analyzing your sequencewith GenomeScan • genes.mit.edu/genomescan/

  12. Assembling Sequence Fragments • Assembling your sequences with CAP3 http://pbil.univ-lyon1.fr/cap3.php • Seqman

  13. All in one DNASTAR • Seqbuilder • Genequest • Protean • Megalign • Primerselect • Seqman • Seqedit

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