Research article
Assessing the ability of sequence-based methods to provide functional insight within membrane integral proteins: a case study analyzing the neurotransmitter/Na+ symporter family
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* Corresponding author: Dennis R Livesay drlivesa@uncc.edu
- † Equal contributors
1 Department of Computer Science and Bioinformatics Research Center, University of North Carolina at Charlotte, Charlotte, NC 28262, USA
2 Biological Sciences Department, California State Polytechnic University, Pomona, CA 91768, USA
3 Department of Computer Science, New Jersey Institute of Technology, Newark, NJ 07102, USA
BMC Bioinformatics 2007, 8:397 doi:10.1186/1471-2105-8-397
Published: 17 October 2007Additional files
Additional file 1:
Phylogenetic tree file. This file contains the raw phylogenetic tree file.
Format: PH Size: 9KB Download file
Additional file 2:
Phylogenetic tree supplementary material. This file contains the phylogenetic tree with bootstrap scores and a list of all experimentally annotated and unannotated leaves.
Format: PDF Size: 2.9MB Download file
This file can be viewed with: Adobe Acrobat Reader
Additional file 3:
Prediction method performance figure. This file contains a plot of accuracy vs. coverage for each prediction method considered. Overall performance values are also provided.
Format: PDF Size: 194KB Download file
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Additional file 4:
Prediction summary figure. This file annotates the LeuTAa sequence with the predictions of each unique method. The sequence is color-coded based on the Intersect results.
Format: PDF Size: 101KB Download file
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Additional file 5:
Leucine-binding pocket figure. This file contains a figure showing the leucine substrate and the three binding pocked residues that are not predicted by any method used herein.
Format: PDF Size: 94KB Download file
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Additional file 6:
Muscle alignment file. This file contains the raw Muscle alignment.
Format: FSA Size: 217KB Download file
Additional file 7:
Alignment supplementary material. This file contains the sum-of-pairs scores for each alignment pair and a series of tables that detail the predictions of each method as a function of alignment input.
Format: PDF Size: 166KB Download file
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Additional file 8:
MINER supplemental figures. This file contains supplementary figures associated with MINER.
Format: PDF Size: 79KB Download file
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Additional file 9:
Prediction threshold summary. This file contains descriptions of performance as a function of threshold level.
Format: PDF Size: 84KB Download file
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