How to find the genomic sequence corresponding to a gene:

  1. Search strategy using the BCM Search launcher
  2. Additional Information: Using Entrez

 A Search Strategy Using the BCM Search Launcher

  1. From the BCM search launcher page choose nucleic acid sequence searches.

  2. For a complete result, you must perform two searches. You have the following search options:


    Search the nr database(1

     and

    Search the unfinished htgs genomic sequence database(2)

    OR

     Search the finished htgs genomic sequencedatabase(3)

     and

    Search the the unfinished htgs genomic sequence database(2)

    Key:

    Select the number corresponding to the search option chosen above

     1   BLASTN / nr dna - Gapped BLASTN with RepeatMasker, Entrez SRS links (NCBI/UW/BCM) [H] [O] [P] [E]
       
     2   BLASTN / Unfinished htgs - Gapped BLASTN with RepeatMasker, Entrez SRS links (NCBI/UW/BCM) [H] [O] [P] [E]
       
     3   BLASTN / Finished htgs - Gapped BLASTN with RepeatMasker, Entrez SRS links (NCBI/UW/BCM) [H] [O] [P] [E]


  3. Enter your DNA sequence in the input box.

  4. Click "Perform search"


Notes on this type of search:

  1. nr database warning: This database contains an extensive amount of data, including finished genomic sequence and cDNAs. Because of the volume of information (i.e. many cDNAs) the actual genomic DNA can be difficult to distinguish within the search results.

  2. htgs (High Throughput Genomic Sequences) database:

    • Unfinished contains only unfinished genomic sequence received into database.

    • Finished contains only finished genomic sequence received into database.



 Additional Information: Using Entrez

An additional, valuble resource is the Entrez database, which contains both finished and unfinished genomic sequence.Entrez is a search engine that integrates information from multiple databases at NCBI. These databases include nucleotide sequences, protein sequences, macromolecular structures, whole genomes, and MEDLINE, through PubMed.

Entrez is only searchable by keyword, however, and thus it requires that an annotation for the genomic sequence be located first. Such an annotation may be found using the search strategy detailed above. The majority of the genomic sequence will have HTG in the keyword field. Any query, such as clone name, gene name, clone library, map locationor sequencing centercan be used in combination with Keyword = HTG to find sequence.

Entrez can be reached through the Baylor Human Genome Sequencing Center:

  1. First select: "Databases and Search Tools"

  2. Then select: "Search Entrez" (listed under "Outside Search Tools and Databases")

    OR .... click here: Entrez




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BCM HGSC