In the postgenomic era, one of the most interesting and important challenges is to understand protein interactions on a large scale. The physical interactions between protein domains are fundamental to the workings of a cell: in multi-domain polypeptide chains, in multi-subunit proteins and in transient complexes between proteins that also exist independently. To study the large-scale patterns ...

We have two objectives. First, we want to build a system for detecting tetratricopeptide repeats in protein sequences. Second, we want to demonstrate how the general bioinformatics database integration system called Kleisli can help build such a system easily. We achieve these two objectives by showing that short and clear programs can be written in Kleisli, using its high-level query language ...

Protein families typically embody a range of related functions and may thus be decomposed into subfamilies with, for example, distinct substrate specificities. Detection of functionally divergent subfamilies is possible by methods for recognizing branches of adaptive evolution in a gene tree. As the number of genome sequences is growing rapidly, it is highly desirable to automatically detect su...

Calpains are ubiquitous and well-conserved proteins that belong to the calcium-dependent, non-lysosomal cysteine protease family. In this study, 8 putative calpains were identified using Pfam domain analysis and BlastP searches in M. oryzae. Three single gene deletion mutants (ΔMocapn7, ΔMocapn9 and ΔMocapn14) and two double gene deletion mutants (ΔMocapn4ΔMocapn7 and ΔMocapn9ΔMocapn7) were obt...

Assignment of all transcription factors (TFs) from genome sequence data is not a straightforward task due to the wide variation in TFs among different species. A DNA binding domain (DBD) and a contiguous non-DBD with a characteristic SCOP or Pfam domain combination are observed in most members of TF families. We found that most of the experimentally verified TFs in prokaryotes are detectable by...

PoInTree (Polar and Interactive Tree) is an application that allows to build, visualize and customize phylogenetic trees in a polar interactive and highly flexible view. It takes as input a FASTA file or multiple alignment formats. Phylogenetic tree calculation is based on a sequence distance method and utilizes the Neighbor Joining (NJ) algorithm. It also allows displaying precalculated trees ...

Sequence-based domain assignment is one of the most important and challenging problems in structural biology. We have developed a method, CHOP, that chops proteins into domain-like fragments. The basic idea is to cut proteins from entirely sequenced organisms beginning from very reliable experimental information (Protein Data Bank), proceeding to expert annotations of domain-like regions (Pfam-...

A central goal of structural genomics is to experimentally determine representative structures for all protein families. At least 14 structural genomics pilot projects are currently investigating the feasibility of high-throughput structure determination; the National Institutes of Health funded nine of these in the United States. Initiatives differ in the particular subset of "all families" on...

The Profile Hidden Markov Model (PHMM) can be poor at capturing dependency between observations because of the statistical assumptions it makes. To overcome this limitation, the dependency between residues in a multiple sequence alignment (MSA) which is the representative of a PHMM can be combined with the PHMM. Based on the fact that sequences appearing in the final MSA are written based on th...