Using MouseBLAST - Basic Steps

This Help document answers questions about how to use the MGI MouseBLAST query form to search a sequence within mouse/rodent sequence databases to find matching sequences that may be associated with mouse genes. Query results may be linked to MGI mouse gene records. Searches are performed using WU-BLAST 2.0. All sequence databases are updated on a weekly basis. Basically, there are five actions:

1. Select a WU-BLAST program.
2. Select a sequence database to search against.
3. Select a repeat masking analysis program (optional).
4. Enter the query sequence.
5. Select the number of results and alignments to show in the output.

Back to Using MouseBLAST - Overview

Use MouseBLAST to search a sequence against a mouse, rat, rodent or human sequence database to find matching sequences. If a matching sequence is associated to an MGI mouse gene record, then summary information about that gene and a link to MGI is inserted in the output.

If any of the matching sequences are associated genes, the result is a display containing links to MGI mouse gene records. All matching sequences have links to the sequence provider's web site. See Search Results for details.

See also:

• Using MouseBLAST - Interpreting the Output Report
• Using MouseBLAST - Sample Queries

The Five Actions

1. Select a WU-BLAST program.

   All six WU-BLAST 2.0 programs are available. Valid combinations of BLAST program with query sequence type, sequence database type, and alignment level are:

   Program	Query Sequence Type	Sequence Database Type	Alignment Level
   BLASTN	DNA	DNA	DNA
   BLASTX	DNA	Protein	Protein
   TBLASTX	DNA	DNA	Protein
   BLASTP	Protein	Protein	Protein
   TBLASTN	Protein	DNA	Protein

2. Select a sequence database to search against.

   See Using MouseBLAST - Sequence Databases for a list of the searchable nucleotide and protein sequence databases.

3. Select a repeat masking analysis program (optional)

   There are several repeat masking programs you can run on your query sequence; these are especially useful when searching with genomic sequence. The following masking options are available.

   • RepeatMasker - Use to mask species-specific repeats in DNA sequences.
   • DUST - Use only with BLASTN searches to mask simple repeats in DNA sequences.
   • SEG - Use to mask low-complexity regions in protein sequences.
   • XNU - Use to mask short tandem repeats in protein sequences.
   For more details, see Using MouseBLAST - Masking Options.


4. Enter the query sequence.

   There are four options for entering a query sequence. You can:

   • Query by sequence accession ID.
     To have MouseBLAST fetch your sequence from one of several sequence databases, enter the correct unique Sequence ID for your sequence and select the respective Sequence Database from the pull-down list. For more details, see Searching By Sequence ID.
   
   
   • Query by genomic sequence interval.
     Note: The build number appearing on the query form is that of the most current NCBI assembly sequence.
     
     1. Click the down-arrow and select the chromosome of interest.
     2. Type or paste the genome coordinates in the box next to between. Separate your entries with either AND or –.
     3. Click the down arrow and select either bp (base pairs) or Mbp (mega base pairs) as the unit of measurement. (The default is to use base pairs.)

     Examples:
     125618206 AND 125622026
     125618206 – 125622026
     125.618 AND 125.622
     125.618 – 125.622

     4. Enter a sequence. Most Web browsers have a limit of 20,000 letters.
        Paste in your sequence in FASTA, GCG, or free-text format. For more details, see Sequence Formats.
     
     
     5. Upload a sequence file.
        To upload the file in FASTA, GCG, or free-text format, enter the local path or click Browse... to navigate your local file system.
   
   
5. Select the number of results and alignments to show in the output.

   Number of scores to show	Limits the number of matching sequences to appear in the summary list at the top of the BLAST results.
   Number of alignments to show	Limits the number of matching sequence alignments to appear in the BLAST results.

For Search results, see Interpreting the MouseBLAST Output Report.

Top