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Open Access Research article

Highly improved homopolymer aware nucleotide-protein alignments with 454 data

Fredrik Lysholm

Author Affiliations

IFM Bioinformatics and SeRC (Swedish e-Science Research Centre), Linköping University, S-581 83, Linköping, Sweden

Department of Cell and Molecular Biology, Science for Life Laboratory, Karolinska Institutet, S-171 77, Stockholm, Sweden

BMC Bioinformatics 2012, 13:230  doi:10.1186/1471-2105-13-230

Published: 12 September 2012

Additional files

Additional file 1:

HAXAT parameter evaluation setup. Name: haxat-parameter-evaluation.zip. Format: Zip compressed evaluation code. Title: HAXAT parameter evaluation setup. The file contains scripts for running the evaluation as well as all the binaries and results included in the manuscript. See the enclosed README for more information.

Format: ZIP Size: 7.6MB Download file

Open Data

Additional file 2:

Figure S1. Double/Single gap penalty ratio for the non-454 aware model. The figure describes the alignment accuracy through Matthews Correlation Coefficient (y-axis) of the homopolymer insertion/deletion recovery versus the double/single gap penalty ratio (x-axis). The accuracy is given for each of the seven degrees of difficulty, i.e. alignments against targets of an identity ranging from 100% down to 40% identity. Furthermore, the mean accuracy for all seven degrees of difficulty, at each gap penalty, is also shown by squares and a dashed line.

Format: TIFF Size: 201KB Download file

Open Data

Additional file 3:

Figure S2. Double/Single gap penalty ratio for the 454-aware model, without flowpeak information. The figure describes the alignment accuracy through Matthews Correlation Coefficient (y-axis) of the homopolymer insertion/deletion recovery versus the double/single gap penalty ratio (x-axis). The accuracy is given for each of the seven degrees of difficulty, i.e. alignments against targets of an identity ranging from 100% down to 40% identity. Furthermore, the mean accuracy for all seven degrees of difficulty, at each gap penalty, is also shown by squares and a dashed line.

Format: TIFF Size: 202KB Download file

Open Data

Additional file 4:

Figure S3. Double/Single gap penalty ratio for the 454-aware model, using flowpeak information. The figure describes the alignment accuracy through Matthews Correlation Coefficient (y-axis) of the homopolymer insertion/deletion recovery versus the double/single gap penalty ratio (x-axis). The accuracy is given for each of the seven degrees of difficulty, i.e. alignments against targets of an identity ranging from 100% down to 40% identity. Furthermore, the mean accuracy for all seven degrees of difficulty, at each gap penalty, is also shown by squares and a dashed line.

Format: TIFF Size: 195KB Download file

Open Data