• 1. Blast 2 Sequences
• This tool produces the alignment of two given sequences using BLAST engine for local alignment.

• 2. BLAST: Basic Local Alignment Search Tool
• NCBI. The "BLAST page" offers a number of different BLAST sequence alignment tools for DNA, RNA or proteins. Use "blastn" for nucleotide BLAST

• 3. ClustalW2
• EBI. Perform alignments of multiple DNA or protein sequences.

• 4. Codon Usage Database
• Kazusa. Find the frequency of codon usage in various organisms.

• 5. dbEST
• NCBI. dbEST is a division of GenBank that contains sequence data and other information on "single-pass" cDNA sequences, or "Expressed Sequence Tags", from a number of organisms

• 6. DDBJ:DNA Data Bank of Japan
• Search for nucleotide sequences. This is one of the 3 databases that make up the International Nucleotide Sequence Database Collaboration

• 7. Eukaryotic Projects - The Institute for Genomic Research (TIGR)
• The TIGR databases contain DNA sequences from a number of eukaryotic and prokaryotic species

• 8. GenBank
• GenBank is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences

• 9. Genomes FASTA - Genomes Similarity Search
• EMBL. Use the FASTA ("Fast All) algorithm to run a nucleotide sequence similarity search

• 10. NCBI Entrez Nucleotide
• NCBI. Search for nucleotide sequences from GenBank, RefSeq and PDB. Retrieves curated and archival (non-curated) sequences from a number of sources. Also allows users to submit nucleotide records.

• 11. NCBI Reference Sequence (RefSeq)
• NCBI. Collection of curated non-redundant reference mRNA sequences within GenBank

• 12. ParAlign
• CMBN Bioinformatics Group and Sencel Bioinformatics. Rapid and sensitive sequence similarity searches powered by parallel computing technology.

• 13. SSEARCH
• DDBJ. Perform a Smith-Waserman alignment search on DNA or protein sequences

• 14. The EMBL Nucleotide Sequence Database
• EBI. Europe's main sequence database. Search for nucleotide sequences or submit them.

• 15. UniSTS
• NCBI. UniSTS is a comprehensive database of sequence tagged sites (STSs) derived from STS-based maps and other experiments. STSs are defined by PCR primer pairs and are associated with additional information such as genomic position, genes, and sequences.