BOL: Related items

FOGSAA: Fast Optimal Global Sequence Alignment Algorithm

Jit — Fri, 08 Dec 2017 14:41:08 -0600

Sequence alignment algorithms are widely used to infer similarirty and the point of differences between pair of sequences. FOGSAA is a fast Global alignment algorithm. It is basically a branch and bound approach which starts branch expansion in a greedy way taking the symbols from the given pair of sequences (protein or nucleotide) and results in an optimal alignment faster than conventional dymanic programming techniques. It is also better than the heuristic methods with respect to alignment quality.

Address of the bookmark: http://www.isical.ac.in/~bioinfo_miu/FOGSAA.htm

Consed--A Finishing Package (BAM File Viewer, Assembly Editor, Autofinish, Autoreport, Autoedit, and Align Reads To Reference Sequence)

Neel — Fri, 07 Feb 2020 07:16:22 -0600

Supports Illumina, 454, other Next-Gen and Sanger Reads and allows mixtures of these read types
Consed includes BamScape which can view bam files with unlimited numbers of reads. BamScape can bring up consed to edit reads and the reference sequence in targeted regions.
Consed is compatible with Newbler, Cross_match, Phrap, MIRA, Velvet and PCAP output.
Quickly takes the user to each variant site for viewing (also available as an automated report)
Overview of assembly can help detect and fix misassemblies
Editing time reduced by the program's ability to pin-point problem areas
Editing is guided by error probabilities

Address of the bookmark: http://www.phrap.org/consed/consed.html

Tools for Sequence translation !

Abhi — Tue, 08 Nov 2022 03:37:58 -0600

BOrf - https://github.com/betsig/borf

CodAn - https://github.com/pedronachtigall/CodAn

EMBOSS-Sixpack - https://www.ebi.ac.uk/Tools/st/emboss_sixpack/

esl-translate - http://hmmer.org/, https://github.com/EddyRivasLab/easel

GeneMarkS-T - http://exon.gatech.edu/GeneMark/license_download.cgi

ORFfinder - https://www.ncbi.nlm.nih.gov/orffinder/ (web server)

PLASS - https://github.com/soedinglab/plass

Prodigal - https://github.com/hyattpd/Prodigal

TransDecoder - https://github.com/TransDecoder/TransDecoder

Tbl2asn: a command-line program that automates the creation of sequence records for submission to GenBank

Poonam Mahapatra — Mon, 29 May 2017 07:37:08 -0500

Tbl2asn is a command-line program that automates the creation of sequence records for submission to GenBank. It uses many of the same functions as Sequin but is driven generally by data files. Tbl2asn generates .sqn files for submission to GenBank. Additional manual editing is not required before submission.

Tbl2asn is available by anonymous FTP. Copy the right version for your platform, then uncompress the file, rename it to "tbl2asn", and set the permissions, as necessary for the platform.

Address of the bookmark: https://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/

Taxoblast : Taxoblast is a pipeline to identify contamination in genomic sequence

Jit — Thu, 23 Nov 2017 08:37:15 -0600

Modern genome sequencing strategies are highly sensitive to contamination making the detection of foreign DNA sequences an important part of analysis pipelines. Here we use Taxoblast, a simple pipeline with a graphical user interface, for the post-assembly detection of contaminating sequences in the published genome of the kelp Saccharina japonica. Analyses were based on multiple blastn searches with short sequence fragments. They revealed a number of probable bacterial contaminations as well as hybrid scaffolds that contain both bacterial and algal sequences. This or similar types of analysis, in combination with manual curation, may thus constitute a useful complement to standard bioinformatics analyses prior to submission of genomic data to public repositories. Our analysis pipeline is open-source and freely available at http://sdittami.altervista.org/taxoblast and via SourceForge (https://sourceforge.net/projects/taxoblast).

Address of the bookmark: https://sourceforge.net/projects/taxoblast/files/

Many-to-many pairwise alignments of two sequence sets

Poonam Mahapatra — Tue, 19 Jun 2018 08:34:15 -0500

needleall reads a set of input sequences and compares them all to one or more sequences, writing their optimal global sequence alignments to file. It uses the Needleman-Wunsch alignment algorithm to find the optimum alignment (including gaps) of two sequences along their entire length. The algorithm uses a dynamic programming method to ensure the alignment is optimum, by exploring all possible alignments and choosing the best. A scoring matrix is read that contains values for every possible residue or nucleotide match. Needleall finds the alignment with the maximum possible score where the score of an alignment is equal to the sum of the matches taken from the scoring matrix, minus penalties arising from opening and extending gaps in the aligned sequences. The substitution matrix and gap opening and extension penalties are user-specified.

Address of the bookmark: http://emboss.sourceforge.net/apps/release/6.6/emboss/apps/needleall.html

SDA: Long-read sequence and assembly of segmental duplications

Jit — Tue, 05 Mar 2019 10:00:57 -0600

Segmental Duplication Assembler (SDA; https://github.com/mvollger/SDA) constructs graphs in which paralogous sequence variants define the nodes and long-read sequences provide attraction and repulsion edges, enabling the partition and assembly of long reads corresponding to distinct paralogs.

https://github.com/mvollger/SDA

Address of the bookmark: https://www.nature.com/articles/s41592-018-0236-3

Miropeats: discovers regions of sequence similarity amongst any set of DNA sequences

Poonam Mahapatra — Mon, 26 Aug 2019 17:55:24 -0500

Miropeats discovers regions of sequence similarity amongst any set of DNA sequences and then presents this similarity information graphically. Sequence similarity searching is a very general tool that forms the basis of many different biological sequence analyses but it is limited by the verbosity of traditional alignment presentation styles. Miropeats enhances the utility of conventional DNA sequence comparisons when looking at long lengths of sequence similarity by summarizing extensive large scale sequence similarities on a single page of graphics. The latest version of Miropeats can be used as a general pairwise alignment program or in its traditional role sorting out a big mess of overlapping or similar regions.

Address of the bookmark: http://www.littlest.co.uk/software/bioinf/old_packages/miropeats/

RePS: Repeat-masked Phrap with scaffolding, a WGS sequence assembler

Jit — Sat, 04 Jan 2020 01:08:09 -0600

RePS (Repeat-masked Phrap with scaffolding), a WGS sequence assembler, that explicitly identifies exact kmer repeats from the shotgun data and removes them prior to the assembly. The established software Phrap is used to compute meaningful error probabilities for each base. Clone-end-pairing information is used to construct scaffolds that order and orient the contigs. The updated version of RePS incorporates some of the ideas introduced by Phusion on clustering

More at

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC186573/

Address of the bookmark: ftp://ftp.genomics.org.cn/pub/ricedb/Tools/RePS/RePS-IBM-AIX.tar.gz

CLARK: Fast, accurate and versatile sequence classification system

Jit — Sat, 15 Feb 2020 01:49:01 -0600

CLARK, a method based on a supervised sequence classification using discriminative k-mers. Considering two distinct specific classification problems (see the article for details), namely (1) the taxonomic classification of metagenomic reads to known bacterial genomes, and (2) the assignment of BAC clones and transcript to chromosome arms/centromeres (in the absence of a finished assembly for the reference genome), CLARK outperforms in classification speed and precision the best state-of-the-art methods.

http://clark.cs.ucr.edu/Spaced/

Address of the bookmark: http://clark.cs.ucr.edu/Spaced/