Related Experiment Video
Updated: Jul 4, 2026

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group
Published on: August 16, 2017
Re-searcher: a system for recurrent detection of homologous protein sequences
Valdemaras Repsys1, Mindaugas Margelevicius, Ceslovas Venclovas
1Institute of Biotechnology, Graiciūno 8, LT-02241 Vilnius, Lithuania. valdemaras@gmail.com
Background:
Sequence searches are routinely employed to detect and annotate related proteins. However, a rapid growth of databases necessitates a frequent repetition of sequence searches and subsequent analysis of obtained results. Although there are several automatic systems available for executing periodical sequence searches and reporting results, they all suffer either from a lack of sensitivity, restrictive database choice or limited flexibility in setting up search strategies. Here, a new sequence search and reporting software package designed to address these shortcomings is described.
Results:
Re-searcher is an open-source highly configurable system for recurrent detection and reporting of new homologs for the sequence of interest in specified protein sequence databases. Searches are performed using PSI-BLAST at desired time intervals either within NCBI or local databases. In addition to searches against individual databases, the system can perform "PDB-BLAST"-like combined searches, when PSI-BLAST profile generated during search against the first database is used to search the second database. The system supports multiple users enabling each to separately keep track of multiple queries and query-specific results.
Conclusions:
Re-searcher features a large number of options enabling automatic periodic detection of both close and distant homologs. At the same time it has a simple and intuitive interface, making the analysis of results even for a large number of queries a straightforward task.
Related Concept Videos
Protein Families
Conservation of Protein Domains Over Different Proteins
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
RNA-seq
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
Homologous Recombination
Conserved Binding Sites
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Directing Proteins to the Rough Endoplasmic Reticulum

