BOL: Related items

HISAT2: a fast and sensitive alignment program for mapping next-generation sequencing reads

Rahul Nayak — Tue, 08 May 2018 04:27:22 -0500

HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome). Based on an extension of BWT for graphs [Sirén et al. 2014], we designed and implemented a graph FM index (GFM), an original approach and its first implementation to the best of our knowledge. In addition to using one global GFM index that represents a population of human genomes, HISAT2 uses a large set of small GFM indexes that collectively cover the whole genome (each index representing a genomic region of 56 Kbp, with 55,000 indexes needed to cover the human population). These small indexes (called local indexes), combined with several alignment strategies, enable rapid and accurate alignment of sequencing reads. This new indexing scheme is called a Hierarchical Graph FM index (HGFM).

more at https://ccb.jhu.edu/software/hisat2/index.shtml

Address of the bookmark: https://github.com/infphilo/hisat2

Gblocks: eliminates poorly aligned positions and divergent regions of a DNA or protein alignment

Poonam Mahapatra — Sat, 02 Jun 2018 07:36:05 -0500

Gblocks eliminates poorly aligned positions and divergent regions of a DNA or protein alignment so that it becomes more suitable for phylogenetic analysis. This server implements the most important features of the Gblocks program to make its use as simple as possible without loosing the functionality that it is necessary in most of the cases. Other options can be changed in the stand-alone program. You can see here an example output file showing the blocks selected from a protein alignment. Further information can be found in the online documentation.

Address of the bookmark: http://molevol.cmima.csic.es/castresana/Gblocks_server.html

Mulan: Multiple-sequence local alignment and visualization for studying function and evolution

Jit — Fri, 24 Aug 2018 09:50:01 -0500

Mulan: Multiple-sequence local alignment and visualization for studying function and evolution

Mulan (http://mulan.dcode.org/), a novel method and a network server for comparing multiple draft and finished-quality sequences to identify functional elements conserved over evolutionary time. Mulan brings together several novel algorithms: the TBA multi-aligner program for rapid identification of local sequence conservation, and the multiTF program for detecting evolutionarily conserved transcription factor binding sites in multiple alignments. In addition, Mulan supports two-way communication with the GALA database; alignments of multiple species dynamically generated in GALA can be viewed in Mulan, and conserved transcription factor binding sites identified with Mulan/multiTF can be integrated and overlaid with extensive genome annotation data using GALA.

Address of the bookmark: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC540288/

MSAProbs - Parallel and accurate multiple sequence alignment

Neel — Tue, 09 Jul 2019 23:58:44 -0500

MSAProbs is a well-established state-of-the-art multiple sequence alignment algorithm for protein sequences. The design of MSAProbs is based on a combination of pair hidden Markov models and partition functions to calculate posterior probabilities. Assessed using the popular benchmarks: BAliBASE, PREFAB, SABmark and OXBENCH, MSAProbs achieves statistically significant accuracy improvements over the existing top performing aligners, including ClustalW, MAFFT, MUSCLE, ProbCons and Probalign. In addition, MSAProbs is optimized for shared-memory CPUs by employing a multi-threaded design, and further parallelized for distributed-memory systems using MPI to overcome high memory overhead barrier and achieve good parallel and data-size scalability.

Address of the bookmark: http://msaprobs.sourceforge.net/homepage.htm#latest

UniAligner: a parameter-free framework for fast sequence alignment

Abhi — Fri, 08 Mar 2024 23:36:12 -0600

UniAligner (formerly, TandemAligner) is the first parameter-free algorithm for sequence alignment that introduces a sequence-dependent alignment scoring that automatically changes for any pair of compared sequences. Classical alignment approaches, such as the Smith-Waterman algorithm, that work well for most sequences, fail to construct biologically adequate alignments of extra-long tandem repeats (ETRs), such as human centromeres and immunoglobulin loci. This limitation was overlooked in the previous studies since the sequences of the centromeres and other ETRs across multiple genomes only became available recently.

More at https://www.nature.com/articles/s41592-023-01970-4

Address of the bookmark: https://github.com/seryrzu/unialigner

Seal: SEquence ALignment evaluation suite

Jit — Wed, 03 Jan 2018 05:05:46 -0600

Seal is a comprehensive sequencing simulation and alignment tool evaluation suite. This software (implemented in Java) provides several utilities that can be used to evaluate alignment algorithms, including:

Reading a pre-existing reference genome from one or more FASTA files.
Alternatively, generating an artificial reference genome based on input parameters (length, repeat count, repeat length, repeat variability rate).
Simulating reads from random locations in the genome based on input parameters of read length, coverage, sequencing error rate, and indel rate.
Applying alignment tools to the genome and the reads through a standardized interface.
Parsing the output of the alignment tool and calculating the number of reads that were correctly or incorrectly mapped.
Computing run times and measures of accuracy.

Seal has interfaces to evaluate the following software packages:

Bowtie
BWA
MAQ
mrFAST
mrsFAST
Novoalign
SHRiMP
SOAPv2

Address of the bookmark: http://compbio.case.edu/seal/

Tiara: deep learning-based classification system for eukaryotic sequences

Rahul Nayak — Mon, 14 Mar 2022 23:02:11 -0500

With a large number of metagenomic datasets becoming available, eukaryotic metagenomics emerged as a new challenge. The proper classification of eukaryotic nuclear and organellar genomes is an essential step toward a better understanding of eukaryotic diversity.

Address of the bookmark: https://academic.oup.com/bioinformatics/article/38/2/344/6375939

PaReBrick: PArallel REarrangements and BReaks identification toolkit

Jit — Fri, 08 Oct 2021 10:20:03 -0500

PaReBrick. The tool takes a collection of strains represented as a sequence of oriented synteny blocks and a phylogenetic tree as input data. It identifies rearrangements, tests them for consistency with a tree, and sorts the events by their parallelism score. The tool provides diagrams of the neighbors for each block of interest, allowing the detection of horizontally transferred blocks or their extra copies and the inversions in which copied blocks are involved.We demonstrated PaReBrick’s efficiency and accuracy and showed its potential to detect genome rearrangements responsible for pathogenicity and adaptation in bacterial genomes

More at https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btab691/6380551

Address of the bookmark: https://github.com/ctlab/parallel-rearrangements

OrthoGNC: A Software for Accurate Identification of Orthologs Based on Gene Neighborhood Conservation

Jit — Tue, 14 Nov 2017 09:30:35 -0600

Orthology relations can be used to transfer annotations from one gene (or protein) to another. Hence, detecting orthology relations has become an important task in the post-genomic era. Various genomic events, such as duplication and horizontal gene transfer, can cause erroneous assignment of orthology relations. In closely-related species, gene neighborhood information can be used to resolve many ambiguities in orthology inference. Here we present OrthoGNC, a software for accurately predicting pairwise orthology relations based on gene neighborhood conservation. Analyses on simulated and real data reveal the high accuracy of OrthoGNC. In addition to orthology detection, OrthoGNC can be employed to investigate the conservation of genomic context among potential orthologs detected by other methods. OrthoGNC is freely available online at http://bs.ipm.ir/softwares/orthognc and http://tinyurl.com/orthoGNC.

http://www.comp.nus.edu.sg/~wongls/projects/orthoGNC/

Address of the bookmark: http://www.sciencedirect.com/science/article/pii/S1672022917301663

Bioinformatics approach to Boar Taint

Rahul Agarwal — Wed, 17 Jul 2013 15:50:37 -0500

Meat products obtained from intact male pigs often produce offensive smell or odour which is recognized as a complex genetic trait called boar taint.Androstenone and Skatole in the fat primarily cause boar taint. Metabolism of androstenone and sex steroids share a common pathway which makes removal of boar taint a very challenging task. Castration is a traditional solution to remove boar taint but it also results in bad quality of meat due to low level of steroids which is objectionable to many consumers. Detected functional variant(s) underlying boar taint compounds can be used as genetic markers in selection of male pigs with reduced boar taint levels. Resequencing of a total of 47 samples belong to Norwegian Landrace (NL) and Duroc (D) pigs with varied boar taint levels were done in Illumina HiSeq2000 to >10X average coverage. Short reads generated from these samples mapped to Sus Scrofa version 10.2 reference assembly using Bowtie2. Alignment file then used for calling SNPs and InDels inside previousy identified QTL regions on SSC5,13, and 7 with the aid of FreeBayes , a variant caller tool. A final list of SNPs was prepared after filtering SNPs on the basis of SNP quality, coverage of SNP allele, functional and structural annotation, and repeats, etc. Selected SNPs will be genotyped in sample population for validation and then used for constructing SNPs haplotypes in close linkage disequilibrium with QTLs and fine mapping of QTLs through association mapping of genotyped SNPs.