Comparison of methods for genomic localization of gene trap sequences

Courtney A Harper¹ , Conrad C Huang² , Doug Stryke² , Michiko Kawamoto² , Thomas E Ferrin¹^,2 and Patricia C Babbitt¹^,2

¹Department of Biopharmaceutical Sciences, University of California San Francisco, 1700 4th Street, San Francisco, CA 94143-2250, USA

²Department of Pharmaceutical Chemistry, University of California San Francisco, 1700 4th Street, San Francisco, CA 94143-2250, USA

author email corresponding author email

BMC Genomics 2006, 7:236doi:10.1186/1471-2164-7-236


Published:	18 September 2006

Additional files

Additional File 1:

An example of errors associated with low signal strength in a 5' RACE sequence. (A) Alignment of trace files for the sequence tags BG-XE342 and BG-XH675, both sequenced with 5' RACE, which localize to protein kinase C binding protein 1 (NCBI accession NM_027230). Black arrows indicate the point of vector insertion. The intensity of the signal diminishes towards the 3' end of each sequence. (B) Enlargement of the green-highlighted regions in A. The reverse complement of the trace sequence, which corresponds to the sequence of the inactivated gene, is listed below the expanded trace plots. The low intensity of the signal in this region of the BG-XH675 trace plot results in two nucleotide assignments, circled in pink, that differ from both genomic sequence from chromosome 2 and the associated mRNA sequence for this gene. In contrast, the corresponding nucleotide assignments in the relatively higher quality BG-XE342 trace plot, also circled in pink, agree with the genomic and mRNA sequences.

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Additional File 2:

Sequence tags. A file of sequence tags aligning to known genes that were used in "Comparison of methods for genomic localization of gene trap sequences". This is a smaller set of sequences than is contained in the International Gene Trap Consortium database (http://www.genetrap.org webcite).

Format: TXT Size: 1.9MB Download file

Additional File 3:

Genes. A file of full-length genes aligning to the sequence tags that were used in "Comparison of methods for genomic localization of gene trap sequences".