Archive - 2008

December 24th

Prediction of DNA-binding residues in proteins from amino acid sequences using a random forest model with a hybrid feature

Prediction of DNA-binding residues in proteins from amino acid sequences using a random forest model with a hybrid feature - Motivation: In this work, we aim to develop a computational approach for predicting DNA-binding sites in proteins from amino acid sequences.

Predicting DNA recognition by Cys2His2 zinc finger proteins

Predicting DNA recognition by Cys2His2 zinc finger proteins - Motivation: Cys2His2 zinc finger (ZF) proteins represent the largest class of eukaryotic transcription factors.

Discovery of phosphorylation motif mixtures in phosphoproteomics data

Discovery of phosphorylation motif mixtures in phosphoproteomics data - Motivation: Modification of proteins via phosphorylation is a primary mechanism for signal transduction in cells.

Slider - maximum use of probability information for alignment of short sequence reads and SNP detection

Slider--maximum use of probability information for alignment of short sequence reads and SNP detection - Motivation: A plethora of alignment tools have been created that are designed to best fit different types of alignment conditions.

KEPE - a motif frequently superimposed on sumoylation sites in metazoan chromatin proteins and transcription factors

KEPE--a motif frequently superimposed on sumoylation sites in metazoan chromatin proteins and transcription factors - Motivation: We noted that the sumoylation site in C/EBP homologues is conserved beyond the canonical consensus sequence for sumoylation.

December 15th

Identification and recovery of minor HIV-1 variants using the heteroduplex tracking assay and biotinylated probes

Identification and recovery of minor HIV-1 variants using the heteroduplex tracking assay and biotinylated probes - We describe a method to identify and recover minor human immunodeficiency virus type 1 (HIV-1) sequence variants from a complex population.

December 5th

Rapid and reliable universal cloning of influenza A virus genes by target-primed plasmid amplification

Rapid and reliable universal cloning of influenza A virus genes by target-primed plasmid amplification - Reverse genetics has become pivotal in influenza virus research relying on rapid generation of tailored recombinant influenza viruses.

Modeling genetic inheritance of copy number variations

Modeling genetic inheritance of copy number variations - Copy number variations (CNVs) are being used as genetic markers or functional candidates in gene-mapping studies.

Identifying molecular markers associated with classification of genotypes by External Logistic Biplots

Identifying molecular markers associated with classification of genotypes by External Logistic Biplots - For characterization of genetic diversity in genotypes several molecular techniques, usually resulting in a binary data matrix, have been used.