Skip to main content

GRDB – Gene Relational DataBase

We have developed a fully automated web service available for the academic community which purpose is to increase the sensitivity of the detection of distantly related protein families. Predicted secondary structure information was added to the information about sequence conservation and variability, a technique known from hybrid threading approaches. The accuracy of the meta profiles created this way is compared with profiles containing only sequence information and with the standard approach of aligning a single sequence with a profile. Additionally, the alignment of meta profiles is more sensitive in detecting remote homology between protein families and more effective than aligning two sequence-only profiles or profile to sequence. The specificity of the alignment score is improved in it’s lower range compared to the robust sequence-only profiles. (More)
Comprehensive classification of nucleotidyltransferase fold proteins: identification of novel families and their representatives in hum

Comments

Popular posts from this blog

NaRCiSuS

Structural genomics is the wide term which describes process of determination of structure representation of information in human genome and at present is limited almost exclusively on proteins. Although in common understanding genetic information means “genes and their encoded protein products”, thousands of human genes produce transcripts which are important in biological point of view but they do not necessarily produce proteins. Furthermore, even though the sequence of the human DNA is known by now, the meaning of the most of the sequences still remains unknown. It is very likely that a large amount of genes has been highly underestimated, mainly because the actual gene finders only work well for large, highly expressed, evolutionary conserved protein-coding genes. Most of those genome elements encode for RNA from which transfer and ribosomal RNAs are the classical examples. But beside these well-known molecules there is a vast unknown world of tiny RNAs that might play a crucial r

Continous integration with PHP and Jenkins

Overview Continuous integration (CI) is a development practice which allows testing, building and checking the quality of the application in automated way without manual developer intervention. It requires developers to integrate code into a shared repository several times a day or every commit/merge to the given branch of the repository. Each check-in is then verified by an automated build, allowing teams to detect problems early. While PHP Continuous Integration (PHPCI) does not require the the code compilation as build” one can understand the set of task like testing and quality checks which are performed in timely manner or when the certain conditions are met. PHPCI can be performed on Jenkins Server. The detailed description of jenkins server configuration in is presented here. PHPCI requires PHing package which can be provided into application by Composer.

GPGPU Accelerated Sparse Linear Solver for Fast Simulation of On-Chip Coupled Problems

Continued device scaling into the nanometer region has given rise to new effects that previously had negligible impact but now present greater challenges to designing successful mixed-signal silicon. Design efforts are further exacebated by unprecedented computational resource requirements for accurate design simulation and verification. This paper presents a GPGPU accelerated sparse linear solver for fast simulation of on-chip coupled problems using nVIDIA and ATI GPGPU accelerators on a multi-core computational cluster and evaluate parallelization strategies from a computational perspective.