DNA Resources

Web Tools

BLAST:

• NCBI

Pairwise and Multiple Alignment – Align multiple sequences (protein, and nucleic acids):

• T-Coffee suite of tools
• Multiple Sequence Alignment tools at EMBL

Sequence Database Searches – Resources that allow users to find sequences based on text or accession number queries:

• NCBI – Global query
• Ensembl
• UCSC Genome Browser

Editing and Publishing – Resources to allow users to modify sequence files for publication and record keeping:

• Vector NTI and Vector NTI Express
• UGENE
• SnapGene Viewer

Phylogeny/Parsimony – Resources to allow the generation trees that provide evolutionary relationship between groups of similar sequences and determine the most probable path of evolution:

• MEGA

Fragment Assembly – Resources to permit users to assemble sequencing projects, excepts sequences, assemble the contigs, and possibly generate a consensus sequence:

• Sequencher

Gene Finding and Pattern Recognition – Resources to allow users to find open reading frames within unknown sequences, patterns in sequences, and get statistics on sequences:

• GLIMMER
• TRANSFAC
• ORF

Primer Selection – Resources to help users design primers for PCR and sequencing:

• Primer3

Translation – Resources to generate a translated peptide from DNA sequences:

• ExPASy
• Tran-seq