The following examples provide the molecular biology researcher with examples on how to do various types of sequence analysis.
  1. Molecular Biology Bookmarks Bookmarks
  2. Keyword Searching Lets say you wish to see if there is a known sequence in the database dealing with Mouse Zebrafish homeobox sequences. If you do not know the accession number or database locusname of the sequence you are interested in, you will need to do a keyword search of the databases. See the following example on keyword searching.Genbank Example
  3. Sequence Searching If you have a sequence and you wish to see what sequences are similar to it, then you should perform a BLAST search. Your query sequence, and the database searched, can be either peptide or nucleic acid in any combination. You can search databases maintained at the National Center for Biotechnology Information (NCBI) in Bethesda, Maryland, USA, or databases on our local computer which are also kept up to date.
    1. BLAST Blast Example
    2. FASTA Fasta Example
    3. Blocks Blocks Example
    4. Other Search Examples Various Examples
  4. Multiple Alignment of sequences After you get the results back from your blast search, you may wish to take the top hits (those with P values smaller than 10E-20) and do a multiple alignment to see if there are regions conserved amongst all of them. We suggest that you use the pima program to do this. After running pima, you can use the mase program to edit the alignment.
    1. pileup pileup Example
    2. pima.sh pima.sh Example
    3. pimaII pimaII Example
    4. clustalw clustalw Example
    5. mase mase Example
  5. Phylogenitic Analysis: Creating Evolutionary Trees After you feel you have a set of related sequences and you wish to perform some phylogenetic analysis to create evolutionary trees, we recommend that you use the PAUP program to construct phylogenetic trees.
    1. PAUP pima-to-paup.sh
  6. Software Recommendations The following is a list of software that is installed on BMERC machines that we recommend for use in sequence analysis.
    1. Software List Software
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    Thomas Graf <tom@darwin.bu.edu>
    Last modified: Thursday, January 21, 1999 3:11:32 PM