Tag Archives: fasta

Tip of the Week: File Format conversion

fileformat_thumbMany of us have worked with DNA and protein sequences of course in several different formats: GenBank and FASTA to name two broadly used ones, but there are many others. Different tools and databases will often require different formats. More often than not, converting from one to the other format isn’t too much of a problem, the database will do it for you, or there will be some help documentation. But this isn’t always the case. There are several ways you can convert formats, for example Galaxy has some limited ability to do this and some databases allow you to export sequence in one of several formats, but often you’ll need a bit more help. ReadSeq is a publicly available software package (downloadable from that link) that will do just that. You could download or install, but EBI also has a web interface for ReadSeq (as do some other services). Today’s tip is for those of you somewhat new to sequence formats (or even some of us who aren’t) and need a quick web interface to converting formats.

New Online Tutorials for Sequence Similarity Search Tools BLAST and FASTA

OpenHelix today announced the availability of new tutorial suites on two highly used sequence similarity search resources: BLAST and FASTA. BLAST, from the National Center for Biotechnology Information (NCBI) at NIH and FASTA, accessed through a web interface at European Bioinformatics Institute (EBI), are both excellent and widely used tools for finding sequence similarities for proteins and nucleic acids.The tutorial suites, available for single purchase or through a low-priced yearly subscription to all OpenHelix tutorials, contain a narrated, self-run, online tutorial, slides with full script, handouts and exercises. With the tutorials, researchers can quickly learn to effectively and efficiently use these resources. These tutorials will teach users:

  • the principles of sequence comparisons
  • basic explanations of scoring matrices and alignments
  • main features of the FASTA and BLAST algorithms
  • how to perform a sequence similarity search
  • how to view and interpret the similarity results
  • how to find additional biological information about matching sequences

To find out more about these and other tutorial suites visit the OpenHelix Tutorial Catalog and OpenHelix or visit the OpenHelix Blog for up-to-date information on genomics. About OpenHelix
OpenHelix, LLC, (http://www.openhelix.com) provides the genomics knowledge you need when you need it. OpenHelix currently provides online self-run tutorials and on-site training for institutions and companies on the most powerful and popular free, web based, publicly accessible bioinformatics resources. In addition, OpenHelix is contracted by resource providers to provide comprehensive, long-term training and outreach programs.