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DNA sequence analysis Xu Cheng. DNA sequence analysis Retrieving DNA sequences from databases Computing nucleotide compositions Identifying restriction.

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Presentation on theme: "DNA sequence analysis Xu Cheng. DNA sequence analysis Retrieving DNA sequences from databases Computing nucleotide compositions Identifying restriction."— Presentation transcript:

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

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5 Sequence quality control Multiple reads on both DNA strands Removing vector sequences Repeat mask

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8 test gi| What’s the vector contamination?

9 Computing/Verifying a Restriction Map REBASE NEBcutter V2.0 Webcutter Restriction Maps dex.html dex.html Just-bio cutter

10 Designing PCR Primers Primer3 Primer-Blast blast/index.cgi?LINK_LOC=BlastHome blast/index.cgi?LINK_LOC=BlastHome

11 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_ )http://www.girinst.org/censor/index.php

12 Finding Protein-Coding Regions ORF Finder at NCBI (AE )http://www.ncbi.nlm.nih.gov/gorf/gorf.htmlhttp://www.ncbi.nlm.nih.gov/gorf/gorf.html

13 Analyzing your DNA sequence with GeneMark exon.gatech.edu/GeneMark/

14 Analyzing your sequence with GenomeScan genes.mit.edu/genomescan/

15 Assembling Sequence Fragments Assembling your sequences with CAP3 Seqman

16 All in one DNASTAR Seqbuilder Genequest Protean Megalign Primerselect Seqman Seqedit


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