The following examples provide the molecular biology
researcher with examples on how to do various types of sequence
- Molecular Biology Bookmarks
- 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
- 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.
- Other Search Examples
- 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.
- 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.
- Software Recommendations
The following is a list of software that is installed on BMERC machines that
we recommend for use in sequence analysis.
BMERC main menu
- Software List
Last modified: Thursday, January 21, 1999 3:11:32 PM