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
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
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
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 http://pbil.univ-lyon1.fr/cap3.php http://pbil.univ-lyon1.fr/cap3.php Seqman
All in one DNASTAR Seqbuilder Genequest Protean Megalign Primerselect Seqman Seqedit
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