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

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Presentation transcript:

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) 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

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

test gi| What’s the vector contamination?

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

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

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_ )

Finding Protein-Coding Regions ORF Finder at NCBI (AE )

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

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

Assembling Sequence Fragments Assembling your sequences with CAP3 Seqman

All in one DNASTAR Seqbuilder Genequest Protean Megalign Primerselect Seqman Seqedit