The Personal Sequence Database: a suite of tools to create and maintain web-accessible sequence databases

Background  

Large molecular sequence databases are fundamental resources for modern bioscientists. Whether for project-specific purposes or sharing data with colleagues, it is often advantageous to maintain smaller sequence databases. However, this is usually not an easy task for the average bench scientist.     

Identification of protein functions using a machine-learning approach based on sequence-derived properties

Background  

Predicting the function of an unknown protein is an essential goal in bioinformatics. Sequence similarity-based approaches are widely used for function prediction; however, they are often inadequate in the absence of similar sequences or when the sequence similarity among known protein sequences is statistically weak. This study aimed to develop an accurate prediction method for identifying protein function, irrespective of sequence and structural similarities.     

A fast algorithm for determining the best combination of local alignments to a query sequence

Background  

Existing sequence alignment algorithms assume that similarities between DNA or amino acid sequences are linearly ordered. That is, stretches of similar nucleotides or amino acids are in the same order in both sequences. Recombination perturbs this order. An algorithm that can reconstruct sequence similarity despite rearrangement would be helpful for reconstructing the evolutionary history of recombined sequences.     

MISHIMA - a new method for high speed multiple alignment of nucleotide sequences of bacterial genome scale data

Background  

Large nucleotide sequence datasets are becoming increasingly common objects of comparison. Complete bacterial genomes are reported almost everyday. This creates challenges for developing new multiple sequence alignment methods. Conventional multiple alignment methods are based on pairwise alignment and/or progressive alignment techniques. These approaches have performance problems when the number of sequences is large and when dealing with genome scale sequences.     

A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure

Background  

Covariance models (CMs) are probabilistic models of RNA secondary structure, analogous to profile hidden Markov models of linear sequence. The dynamic programming algorithm for aligning a CM to an RNA sequence of length N is O(N ³) in memory. This is only practical for small RNAs.     

BrEPS: a flexible and automatic protocol to compute enzyme-specific sequence profiles for functional annotation

Background  

Models for the simulation of metabolic networks require the accurate prediction of enzyme function. Based on a genomic sequence, enzymatic functions of gene products are today mainly predicted by sequence database searching and operon analysis. Other methods can support these techniques: We have developed an automatic method "BrEPS" that creates highly specific sequence patterns for the functional annotation of enzymes.     

ProFAT: a web-based tool for the functional annotation of protein sequences

Background  

The functional annotation of proteins relies on published information concerning their close and remote homologues in sequence databases. Evidence for remote sequence similarity can be further strengthened by a similar biological background of the query sequence and identified database sequences. However, few tools exist so far, that provide a means to include functional information in sequence database searches.     

LipocalinPred: a SVM-based method for prediction of lipocalins

Background  

Functional annotation of rapidly amassing nucleotide and protein sequences presents a challenging task for modern bioinformatics. This is particularly true for protein families sharing extremely low sequence identity, as for lipocalins, a family of proteins with varied functions and great diversity at the sequence level, yet conserved structures.     

Library on a slide for bacterial comparative genomics

Background  

We describe a novel application of microarray technology for comparative genomics of bacteria in which libraries of entire genomes rather than the sequence of a single genome or sets of genes are arrayed on the slide and then probed for the presence or absence of specific genes and/or gene alleles.     

Occurrence of protein structure elements in conserved sequence regions

Background  

Conserved protein sequence regions are extremely useful for identifying and studying functionally and structurally important regions. By means of an integrated analysis of large-scale protein structure and sequence data, structural features of conserved protein sequence regions were identified.     

Enzyme classification with peptide programs: a comparative study

Background  

Efficient and accurate prediction of protein function from sequence is one of the standing problems in Biology. The generalised use of sequence alignments for inferring function promotes the propagation of errors, and there are limits to its applicability. Several machine learning methods have been applied to predict protein function, but they lose much of the information encoded by protein sequences because they need to transform them to obtain data of fixed length.     

A configuration space of homologous proteins conserving mutual information and allowing a phylogeny inference based on pair-wise Z-score probabilities

Background  

Popular methods to reconstruct molecular phylogenies are based on multiple sequence alignments, in which addition or removal of data may change the resulting tree topology. We have sought a representation of homologous proteins that would conserve the information of pair-wise sequence alignments, respect probabilistic properties of Z-scores (Monte Carlo methods applied to pair-wise comparisons) and be the basis for a novel method of consistent and stable phylogenetic reconstruction.     

PLAN: a web platform for automating high-throughput BLAST searches and for managing and mining results

Background  

BLAST searches are widely used for sequence alignment. The search results are commonly adopted for various functional and comparative genomics tasks such as annotating unknown sequences, investigating gene models and comparing two sequence sets. Advances in sequencing technologies pose challenges for high-throughput analysis of large-scale sequence data. A number of programs and hardware solutions exist for efficient BLAST searching, but there is a lack of generic software solutions for mining and personalized management of the results. Systematically reviewing the results and identifying information of interest remains tedious and time-consuming.     

Functional annotation by identification of local surface similarities: a novel tool for structural genomics

Background  

Protein function is often dependent on subsets of solvent-exposed residues that may exist in a similar three-dimensional configuration in non homologous proteins thus having different order and/or spacing in the sequence. Hence, functional annotation by means of sequence or fold similarity is not adequate for such cases.     

Accuracy of structure-based sequence alignment of automatic methods

Background  

Accurate sequence alignments are essential for homology searches and for building three-dimensional structural models of proteins. Since structure is better conserved than sequence, structure alignments have been used to guide sequence alignments and are commonly used as the gold standard for sequence alignment evaluation. Nonetheless, as far as we know, there is no report of a systematic evaluation of pairwise structure alignment programs in terms of the sequence alignment accuracy.     

Importin alpha binding and nuclear localization of PARP-2 is dependent on lysine 36, which is located within a predicted classical NLS

Background  

The enzymes responsible for the synthesis of poly-ADP-ribose are named poly-ADP-ribose polymerases (PARP). PARP-2 is a nuclear protein, which regulates a variety of cellular functions that are mainly controlled by protein-protein interactions. A previously described non-conventional bipartite nuclear localization sequence (NLS) lies in the amino-terminal DNA binding domain of PARP-2 between amino acids 1–69; however, this targeting sequence has not been experimentally examined or validated.     

GPR99, a new G protein-coupled receptor with homology to a new subgroup of nucleotide receptors

Background  

Based on sequence similarity, the superfamily of G protein-coupled receptors (GPRs) can be subdivided into several subfamilies, the members of which often share similar ligands. The sequence data provided by the human genome project allows us to identify new GPRs by in silico homology screening, and to predict their ligands.