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The alignment of protein superfamily sequences Part I: Identifying Cluster Specific Subsequences (CSS) in Protein Families
(A2B2C, 2015-10-14)
Multiple Sequence Alignments (MSA) are crucial tools in protein bioinformatics. Despite recent advances such as obtained by MAFFT and Promals3D, MSA construction of complex superfamilies remains problematic and requires ...
miRNAfe: a tool for feature extraction in pre-miRNA prediction
(A2B2C, 2015-10-14)
MicroRNAs (miRNA) are a group of short (~22 nucleotides) non-coding RNA which can play important roles in gene regulation by targeting mRNAs for cleavage or translational repression. Precursors of miRNA (pre-miRNA) are ...
miRNAss: a semi-supervised approach for microRNA prediction
(A2B2C, 2015-10-14)
MicroRNA (miRNAs) play essential roles in post-transcriptional gene regulation in animals and plants. Precursors of miRNA (pre-miRNA) are characterized by their hairpins structure. However, a large amount of similar sequences ...
PATENA: an algorithm for the design of protein linker sequences
(A2B2C, 2015-10-14)
The successful construction of multidomain fusion proteins requires a linker sequence to covalently join the selected domains. Usual requirements for this sequence are to lack any interfering functional feature and the ...
Prediction of peptide-MHC class II binding affinity with improved binding core identification; implications for the interpretation of T cell cross-reactivity
(A2B2C, 2015-10-14)
Prediction of peptide-MHC class II binding involves answering two questions: does the peptide bind to the MHC, and if so, where does it bind. Addressing the first question, prediction of binding affinity for MHC class II ...
The alignment of protein superfamily sequences Part II: Multiple Alignment Touch-up Engine (MATE)
(A2B2C, 2015-10-14)
Multiple Sequence Alignments (MSA) are crucial tools in protein bioinformatics. Despite recent advances, construction of MSAs for complex superfamilies remains problematic and requires rigorous manual correction. In this ...
Development of an algorithm to predict HIV-1 tropism from V3 loop sequence for BF subtype
(A2B2C, 2015-10-14)
HIV tropism can be X4 or R5 according to the co-receptor usage for viral entry into CD4+ T cells. This interaction involves the V3 loop region of viral glycoprotein gp120, coded in the env gene. The determination of viral ...
Estimation of independence between discrete and continuous data sets
(A2B2C, 2015-10-14)
Mutual Information (MI) is an entropic measure of the relationship of two random variables, X,Y. MI is defined as the relative entropy or Kullback Leibler distance [1,2] between the joint distribution and the product of ...
Molecular characterization of novel β-globin variants associated to dominant β-thalassemia
(A2B2C, 2015-10-14)
The β-thalassemias (β-thal) (OMIM: 613985) are a group of blood disorders characterized by reduced synthesis of β-globin chains, and hence a diminished production of hemoglobin. We describe here the physicochemical, ...
Genome-wide identification of microRNAs and their targets in the zoonotic parasite Echinococcus canadensis
(A2B2C, 2015-10-14)
MicroRNAs (miRNAs), a class of small non-coding RNAs, are key regulators of gene expression at post-transcriptional level and play essential roles in biological processes such as development and metabolism. MiRNAs silence ...