Performing a Sequence Alignment from an Accession Number

Biochemistry, Molecular Biology, and Cell Biology Protocols >>Performing a Sequence Alignment from an Accession Number

1. Enter the accession number of the nucleic acid or amino acid sequence from NCBI or other database, and obtain the sequence in FASTA format. Alternatively, search for the accession number and sequence by entering the name of the protein or gene.
2. Enter the sequences obtained into a program such as ClustalW or Blast.
3. Sequences in areas with a high degree of conservation indicate that they are likely important for function or structure. Conservation can mean having basic residues the same (eg Lysines, Arginines) or acidic residues the same (eg Glutamate, Aspartate), or having a similar side chain size (eg Cysteine, Serine)
4. Sequences in areas with a low degree of conservation indicate that they may be important for variability and specificity.
5. One set of sequences important to align would be the DNA or protein sequences of the same molecule in different species. Another would be to align the same family members of a particular domain.