Segtor: Rapid Annotation of Genomic Coordinates and Single Nucleotide Variations Using Segment Trees

Abstract

Various research projects often involve determining the relative position of genomic coordinates, intervals, single nucleotide variations (SNVs), insertions, deletions and translocations with respect to genes and their potential impact on protein translation. Due to the tremendous increase in throughput brought by the use of next-generation sequencing, investigators are routinely faced with the need to annotate very large datasets. We present Segtor, a tool to annotate large sets of genomic coordinates, intervals, SNVs, indels and translocations. Our tool uses segment trees built using the start and end coordinates of the genomic features the user wishes to use instead of storing them in a database management system. The software also produces annotation statistics to allow users to visualize how many coordinates were found within various portions of genes. Our system currently can be made to work with any species available on the UCSC Genome Browser. Segtor is a suitable tool for groups, especially those with limited access to programmers or with interest to analyze large amounts of individual genomes, who wish to determine the relative position of very large sets of mapped reads and subsequently annotate observed mutations between the reads and the reference. Segtor (http://lbbc.inca.gov.br/segtor/) is an open-source tool that can be freely downloaded for non-profit use. We also provide a web interface for testing purposes.

Binding Sites Analyser (BiSA): Software for Genomic Binding Sites Archiving and Overlap Analysis

“…Existing methods of finding overlaps such as BEDTools, UCSC Table Browser, Homer or Segtor [4] , [5] , [6] are limited in functionality for simultaneous comparison to multiple archived data sets. Moreover, few tools provide a simple interface that can be easily implemented by biologists with limited computing skills.…”

E-TALEN: a web tool to design TALENs for genome engineering

“…Annotation of many putative binding sites requires an efficient search of genome annotations. To maximize efficiency and shorten running time, a binary interval tree approach (16) has been used, whereby all genome annotations for the respective organism are stored as a binary interval tree (Supplementary Figure S1). This is an efficient way to store and retrieve interval information and to reduce runtime complexity for the query to O(log(n)), where n is the number of searched intervals.…”

“…This is an efficient way to store and retrieve interval information and to reduce runtime complexity for the query to O(log(n)), where n is the number of searched intervals. This idea has been successfully applied in annotating short sequencing reads after mapping (16). During the process of target site identification all putative hits are filtered by their nucleotide composition and the acquired annotations according to the user’s requirements (4).…”

Bioinformatics of Cancer ncRNA in High Throughput Sequencing: Present State and Challenges

“…One exception is the RandA pipeline (Isakov et al, 2012), that uses the whole Rfam database, and can be applied to different ncRNAs. Segtor (Renaud et al, 2011) is another tool that works to assist in one important step in the biological interpretation effort of every HTS experiment. Segtor allows the fast annotation of sequences from a given HTS experiment and provide a list of ncRNA genes affected by multiple types of nucleotide polymorphisms.…”