Using MouseBLAST - Sample Queries
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This help document describes the following sample searches:

The following examples identify the field values to set for the query. Default values for any other fields are assumed.

Find mouse protein sequences similar to Bmp2

BMPs (bone morphogenic proteins) are a large family, so there should be many similar sequences. Enter or select the following on the MouseBLAST query form and from the results, follow links to MGI gene reports.

BLAST Program:BLASTP
Database:UniProt Mouse
Masking Options
For protein queries:Check both SEG and XNU
Query sequence
Sequence ID:P21274
Sequence database:SWISS-PROT
Output options
Number of scores to show:10
Number of alignments to show:100
Results

If you do not check the box at the bottom of the query form (Exclude alignment of query sequence...), the first match may be to the query sequence itself (if the database you searched contains it). You can:

Find genes located within specific assembly coordinates

You know that the kit oncogene is located on chromosome 5 and that the coordinates are somewhere between 75,200,000 and 75,400,000. Locate Option 2 in the Query sequence section of the query form (Query by genomic sequence interval), and enter your information.

Chromosome:5
Coordinates between 75,200,000 - 75,400,000 (or 75,200,000 AND 75,400,000)
Number of scores to show:25
Number of alignments to show:25
Results

The results are similar in appearance to those for Example 1. Follow the links to see the various gene records for kit.

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Determine whether a sequence region from a strain other than C57BL/6 contains regions of similarity to sequences associated with MGI mouse genes

When searching with a genomic sequence, use RepeatMasker to filter any repeats. The sequence below is a Mus musculus chromosome 1 genomic contig, strain 129/SvEvTac, GenBank entry, NT_039193.

MouseBLAST Query Results 

BLASTN 2.0MP-WashU [04-May-2006] [sol8-ultra-ILP32F64 2006-05-04T16:04:21] (WU-BLAST information)
Query= QUERY QUERY Database: /data/seqdbs/blast/gb.new/gbmus 99,787 sequences; 260,597,413 total letters.  
WARNING: Use of the hspsepSmax parameter should be considered with long database sequences, to improve 
the biological relevance of the HSP groups that are assembled and to improve the statistical 
discrimination of these groups from random background.   
Smallest Sum High Probability Sequences producing High-scoring Segment Pairs: Score P(N) N

For the selected sequences

 gb|AK052447.1|AK052447 Mus musculus 13 days embryo lung c... 8136 0.        1
      MGI:98297 Shh sonic hedgehog (Chr 5)
 gb|AK077688.1|AK077688 Mus musculus 8 days embryo whole b... 8021 0.        1
      MGI:98297 Shh sonic hedgehog (Chr 5)
 gb|BC063087.1|BC063087 Mus musculus sonic hedgehog, mRNA ... 8015 0.        1
      MGI:98297 Shh sonic hedgehog (Chr 5)
 gb|X76290.1|MMSHH M.musculus (C57BL/6J) Shh mRNA.            3765 7.0e-165  1
      MGI:98297 Shh sonic hedgehog (Chr 5)
 gb|AK032466.1|AK032466 Mus musculus adult male olfactory ...  505 9.0e-13   1
      MGI:94891 Dhh desert hedgehog (Chr 15)
 gb|X76292.1|MMDHH M.musculus (129/Su) Dhh gene.               491 1.4e-12   1
      MGI:94891 Dhh desert hedgehog (Chr 15)
 gb|AK033392.1|AK033392 Mus musculus 16 days embryo lung c...  491 3.1e-12   1
      MGI:94891 Dhh desert hedgehog (Chr 15)
 gb|X76291.1|MMIHH M.musculus (C57BL/6J) Ihh mRNA.             459 2.9e-11   1
      MGI:96533 Ihh Indian hedgehog (Chr 1)
 gb|U85610.1|MMU85610 Mus musculus Indian hedgehog protein...  459 8.6e-11   1
      MGI:96533 Ihh Indian hedgehog (Chr 1)
 gb|BC046984.1|BC046984 Mus musculus Indian hedgehog, mRNA...  459 9.4e-11   1
      MGI:96533 Ihh Indian hedgehog (Chr 1)
 gb|AL732560.11|AL732560 Mouse DNA sequence from clone RP2...  373 1.1e-06   1
      MGI:1918877 4833420G11Rik RIKEN cDNA 4833420G11 gene (Chr 2)
      MGI:1344352 Dido1 death inducer-obliterator 1 (Chr 2)
 gb|U37545.1|MMU37545 Mus musculus steroid sulfatase (Sts)...  360 3.1e-06   1
      MGI:98438 Sts steroid sulfatase (Chr XY)
 gb|BC060099.1|BC060099 Mus musculus zinc finger protein 3...  359 4.0e-06   1
      MGI:1860402 Zfp316 zinc finger protein 316 (Chr 5)
 gb|BC057078.1|BC057078 Mus musculus zinc finger protein 3...  359 4.1e-06   1
      MGI:1860402 Zfp316 zinc finger protein 316 (Chr 5)
 gb|AK047201.1|AK047201 Mus musculus 10 days neonate cereb...  357 4.4e-06   1
      MGI:1930001 Bhlhb5 basic helix-loop-helix domain containing, class B5 (Chr 3)
 gb|AK076228.1|AK076228 Mus musculus 16 days embryo head c...  353 7.1e-06   1
      MGI:1930001 Bhlhb5 basic helix-loop-helix domain containing, class B5 (Chr 3)
 gb|AF082568.1|AF082568 Mus musculus zinc finger type tran...  354 7.1e-06   1
      MGI:1860402 Zfp316 zinc finger protein 316 (Chr 5)
 gb|BC053007.1|BC053007 Mus musculus basic helix-loop-heli...  353 7.1e-06   1
      MGI:1930001 Bhlhb5 basic helix-loop-helix domain containing, class B5 (Chr 3)
 gb|X66367.1|MMGLUR M.musculus gene for glucocorticoid rec...  341 2.7e-05   1
      MGI:95824 Nr3c1 nuclear receptor subfamily 3, group C, member 1 (Chr 18)
 gb|AF031955.1|AF031955 Mus musculus krupple-related zinc ...  331 7.5e-05   1
      MGI:1860402 Zfp316 zinc finger protein 316 (Chr 5)
 gb|AF218865.1|AF218865 Mus musculus BETA3 mRNA, complete ...  323 0.00016   1
      MGI:1930001 Bhlhb5 basic helix-loop-helix domain containing, class B5 (Chr 3)
 gb|AK173265.1|AK173265 Mus musculus mRNA for mKIAA1791 pr...  324 0.00016   1
      MGI:1916812 Cdc2l5 cell division cycle 2-like 5 (cholinesterase-related cell division controller) (Chr 13)
 gb|AF190578.1|AF190578 Mus musculus receptor for viral-en...  319 0.00027   1
      MGI:1890127 Plxnc1 plexin C1 (Chr 10)
 gb|BC054540.1|BC054540 Mus musculus neogenin, mRNA (cDNA ...  315 0.00042   1
      MGI:1097159 Neo1 neogenin (Chr 9)
 gb|U44942.1|MMU44942 Mus musculus recombinant quaking gen...  307 0.00091   1
      MGI:97837 Qk quaking (Chr 17)

WARNING:  Descriptions of 139 database sequences were not reported due to the
          limiting value of parameter V = 25
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