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

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

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

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

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

10. Designing PCR Primers Primer3 http://frodo.wi.mit.edu/http://frodo.wi.mit.edu/ Primer-Blast http://www.ncbi.nlm.nih.gov/tools/primer- blast/index.cgi?LINK_LOC=BlastHome http://www.ncbi.nlm.nih.gov/tools/primer- 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_004559.13 )http://www.girinst.org/censor/index.php

12. Finding Protein-Coding Regions ORF Finder at NCBI (AE008569 )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 http://pbil.univ-lyon1.fr/cap3.php http://pbil.univ-lyon1.fr/cap3.php Seqman

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