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What can BLAST 2 Sequences do for me?

(Use BLAST 2 Sequences to look for mismatches between two nucleotide sequences)

  Sample User Question
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Sample User Question back to top

Use the program BLAST 2 Sequences to compare the RefSeq mRNA for CCAAT/enhancer binding protein (C/EBP), delta CEBPD (NM_005195) with the model transcript (found here) predicted from the human genome. (Note: You will need to turn filtering off to get the complete alignment). Are there any mismatches? Do these mismatches affect the model protein sequence compared to the reference sequence?

Analysis/Comments back to top

Why is BLAST 2 Sequences useful? There are many instances where the ability to compare two sequences without having to do a complete BLAST search of a database is useful, especially in an instance like this one where the function of a contstruct may be in question.

Step By Step Guide back to top

BLAST 2 Sequences

  • Paste the accession numbers from NM_005195 and XM_005023 in the appropriate boxes on the BLAST 2 Sequences page.
  • Click the check box next to the Filter option to turn filtering off.
  • Click the Align button.
  • View the one difference in the two sequences. This difference is in the coding region of the gene and would cause a frame-shift mutation in the translation.
  • To see the results of the frame-shift between the two resulting protein sequences run BLAST 2 Sequences again with the translation products of the two nucleotide sequences (found here.) (Translation products were generated using the Translate Tool from ExPASy.)

Additional Notes back to top

As mentioned in the BLAST 2 Sequences slide of this module, BLAST 2 Sequences is based upon BLAST – local alignment – and is therefore not very useful when two sequences are highly, or even moderately, divergent.

This question originally used the genomic sequence derived from GenBank that had the single nucleotide missing. This sequence, XM_005023 has been marked as being removed due to standard genome annotation processing.

Thanks for this question to Peter Cooper. More of Peter's excellent questions can be found at The Field Guide Problem Set.

Similarity Searching/BLAST 2 Sequences User Question Back to the Question Revised 07/22/05