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Pavle Goldstein

Publications and source records attributed to Pavle Goldstein.

3 recordsLinked to original sources
arXiv2022

A Clique-Based Method for Improving Motif Scanning Accuracy

We present a new approach for improving motif scanning accuracy, based on analysis of in-between similarity. Given a set of motifs obtained from a scanning process, we construct an associated weighted graph. We also compute the expected weight of an edge in such a graph. It turns out that restricting results to the maximal clique in the graph, computed with respect to the expected weight, greatly increases precision, hence improves accuracy of the scan. We tested the method on an ungapped motif-characterized protein family from five plant proteomes. The method was applied to three iterative motif scanners - PSI-BLAST, JackHMMer and IGLOSS - with very good results

q-bio.QM↗
arXiv2018

IGLOSS: iterative gapless local similarity search

Searching for local sequence patterns is one of the basic tasks in bioinformatics. Sequence patterns might have structural, functional or some other relevance, and numerous methods have been developed to detect and analyze them. These methods often depend on the wealth of information already collected. The explosion in the number of newly available sequences calls for novel methods to explore local sequence similarity. We have developed a high sensitivity web-based iterative local similarity scanner, that finds sequence patterns similar to a submitted query.

q-bio.QM↗