BOL: Related items

Mercator: Multiple Whole-Genome Orthology Map Construction

Jit — Tue, 19 May 2020 16:46:22 -0500

Whole-genome homology maps attempt to identify the evolutionary relationships between and within multiple genomes. The term "syntenic" is often used to describe regions of multiple genomes that are believed to have evolved from the same region in an ancestral genome. However, it has been pointed out that this use of the term is incorrect (Passarge et al. 1999) and thus we will use the terms "homologous", "orthologous", and "paralogous" instead. Ideally, given K genomes, we would like to identify all orthologous genomic regions as well as paralogous regions within each genome and hypothetical ancestral genome. Maps listing these relationships are extremely valuable to researchers performing comparative analyses of genomic sequence. Here we present our initial work in the form a program called Mercator that constructs orthology maps between multiple whole genomes.

Address of the bookmark: https://www.biostat.wisc.edu/~cdewey/mercator/

Apollo: a sequence annotation editor

Abhimanyu Singh — Tue, 27 Aug 2019 08:08:47 -0500

The well-established inaccuracy of purely computational methods for annotating genome sequences necessitates an interactive tool to allow biological experts to refine these approximations by viewing and independently evaluating the data supporting each annotation. Apollo was developed to meet this need, enabling curators to inspect genome annotations closely and edit them

Address of the bookmark: https://genomebiology.biomedcentral.com/articles/10.1186/gb-2002-3-12-research0082

Sibelia: A comparative genomics tool

BioStar — Sat, 22 Aug 2020 02:49:00 -0500

Sibelia: A comparative genomics tool: It assists biologists in analysing the genomic variations that correlate with pathogens, or the genomic changes that help microorganisms adapt in different environments. Sibelia will also be helpful for the evolutionary and genome rearrangement studies for multiple strains of microorganisms.

Sibelia is useful in finding: (1) shared regions, (2) regions that present in one group of genomes but not in others, (3) rearrangements that transform one genome to other genomes.

More at http://bioinf.spbau.ru/sibelia

Sibelia docs http://gensoft.pasteur.fr/docs/Sibelia/3.0.7/SIBELIA.md

Address of the bookmark: https://github.com/bioinf/Sibelia

Kraken: ultrafast metagenomic sequence classification using exact alignments

Jit — Mon, 27 Jun 2016 11:01:44 -0500

Kraken is an ultrafast and highly accurate program for assigning taxonomic labels to metagenomic DNA sequences. Previous programs designed for this task have been relatively slow and computationally expensive, forcing researchers to use faster abundance estimation programs, which only classify small subsets of metagenomic data. Using exact alignment of k-mers, Kraken achieves classification accuracy comparable to the fastest BLAST program. In its fastest mode, Kraken classifies 100 base pair reads at a rate of over 4.1 million reads per minute, 909 times faster than Megablast and 11 times faster than the abundance estimation program MetaPhlAn. Kraken is available at http://ccb.jhu.edu/software/kraken/.

Krona

https://sourceforge.net/p/krona/home/krona/

Address of the bookmark: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4053813/

CRBHits: From Conditional Reciprocal Best Hits to Codon Alignments and Ka/Ks in R

Shruti Paniwala — Wed, 11 Nov 2020 23:06:03 -0600

CRBHits is a coding sequence (CDS) analysis pipeline in R (R Core Team, 2019). It reimplements the Conditional Reciprocal Best Hit (CRBH) algorithm crb-blast and covers all necessary steps from sequence similarity searches, codon alignments to Ka/Ks calculations and synteny. The new R package targets ecology, population and evolutionary biologists working in the field of comparative genomics.

Address of the bookmark: https://gitlab.gwdg.de/mpievolbio-it/crbhits

pbalign: maps PacBio reads to reference sequences and saves alignments to a BAM file

Jit — Thu, 24 May 2018 10:06:52 -0500

pbalign aligns PacBio reads to reference sequences, filters aligned reads according to user-specific filtering criteria, and converts the output to either the SAM format or PacBio Compare HDF5 (e.g., .cmp.h5) format. The output Compare HDF5 file will be compatible with Quiver if --forQuiver option is specified.

Address of the bookmark: https://github.com/PacificBiosciences/pbalign

BLAST options, setting and defaults

Jit — Mon, 10 Dec 2018 08:29:37 -0600

BLAST stands for Basic Local Alignment Search Tool and was developed by Altschul et al. (1990) and significantly improved by Altschul et al. (1997). It is a very fast search algorithm that is used to separately search protein or DNA databases. BLAST is best used for sequence similarity searching, rather than for motif searching. For searches using a query sequence of fewer than twenty residues, PatMatch is the best choice. Another sequence alignment tool that may yield different results from BLAST, and may be useful for motif searching, is FASTA. To search nonplant datasets, try NCGR BLAST or NCBI BLAST.

A fairly complete on-line guide to BLAST searching can be found at the NCBI BLAST Help Manual. For a theoretical overview of BLAST, see the NCBI BLAST Course. Additional information can be found in the BLAST 2.0 Release Notes

	BLASTN	BLASTP	BLASTX	TBLASTN	TBLASTX	PSIBLAST
Gap opening penalty: cost to open a gap [integer]	default = 5	default = 11 limited values are supported	default = 11 limited values are supported	default = 11 limited values are supported	default = 11 limited values are supported	default = 5
Gap extension penalty: cost to extend a gap [integer]	default = 2	default = 1 a 0 in this field means to use the default	default = 1 a 0 in this field means to use the default	default = 1 a 0 in this field means to use the default	default = 1 a 0 in this field means to use the default	default = 2
Nucleic match: reward for a match in the BLAST portion of run [integer]	default = 1	n/a	n/a	n/a	n/a	default = 1
Nucleic mismatch: penalty for a mismatch in the blast portion of run [integer]	default = -3	n/a	n/a	n/a	n/a	default = -3
Expectation value: (E) [real]	default = 10.0	default = 10.0	default = 10.0	default = 10.0	default = 10.0	default = 10.0
Word size: the size of the initial word that must be matched between the database and the query sequence	default = 11	default = 3	default = 3	default = 3	default = 3	default = 11
Max scores: Number of one-line descriptions (V) [Integer]	default = 25	default = 25	default = 25	default = 25	default = 25	default = 25
Max alignments: number of alignments to show (B) [integer]	default = 15	default = 15	default = 15	default = 15	default = 15	default = 15
Query filter: filter applied to the query sequence	default = DUST	default = SEG	default = SEG	default = SEG	default = SEG	default = DUST
Query genetic code: genetic code to be used in BLASTX translation of the query	n/a	n/a	default = universal	default = universal	default = universal	n/a
Matrix: substitution matrix to be used for amino acid comparisons	no default	default = blosum62	default = blosum62	default = blosum62	default = blosum62	no default

Supported and Suggested Values for Gap Open and Extension in BLASTP, BLASTX, TBLASTN, and TBLASTX

Gaps Open	Gap Extension
10	1
10	2
11	1
8	2
9	2

Address of the bookmark: https://www.arabidopsis.org/Blast/BLASToptions.jsp

GAM-NGS: genomic assemblies merger for next generation sequencing

Jit — Fri, 19 May 2017 07:44:14 -0500

GAM-NGS is a tool able to merge two or more assemblies in order to improve contiguity and correctness. It can be used on all NGS-based assembly projects and it shows its full potential with multi-library Illumina-based projects. With more than 20 available assemblers it is hard to select the best tool. In this context we propose a tool that improves assemblies (and, as a by-product, perhaps even assemblers) by merging them and selecting the generating that is most likely to be correct.

Address of the bookmark: https://github.com/vice87/gam-ngs

CAMSA :: a tool for Comparative Analysis and Merging of Scaffold Assemblies

Rahul Nayak — Thu, 28 Dec 2017 09:10:26 -0600

CAMSA – is a tool for Comparative Analysis and Merging of Scaffold Assemblies, distributed both as a standalone software package and as Python library under the MIT license.

Main features:

works with any number of scaffold assemblies in de-novo non-progressive fashion
allows to simultaneously work with scaffold assemblies obtained from any in silico and in vitro techniques, supporting multiple existing formats via built-in converters
creates an extensive report with several comparative quality metrics (both on assembly level and on the level of individual assembly points)
constructs a merged combined scaffold assembly
provides an interactive framework for a visual comparative analysis of the given assemblies

Address of the bookmark: https://cblab.org/camsa/

Metassembler: merging and optimizing de novo genome assemblies

Rahul Nayak — Tue, 08 May 2018 04:52:33 -0500

Metassembler combines multiple whole genome de novo assemblies into a combined consensus assembly using the best segments of the individual assemblies.

Genome assembly projects typically run multiple algorithms in an attempt to find the single best assembly, although those assemblies often have complementary, if untapped, strengths and weaknesses. We present our metassembler algorithm that merges multiple assemblies of a genome into a single superior sequence.

Address of the bookmark: https://sourceforge.net/projects/metassembler/?source=directory