BOL: Related items

Introduction to programming. Write short programs that generate graphics and animation.

Ram Yash Pal — Thu, 14 Aug 2014 23:29:04 -0500

Introduction to programming. Write short programs that generate graphics and animation.

http://funprogramming.org/

BEAP: Blast Extension and Assembly Program

Shruti Paniwala — Mon, 11 Jun 2018 04:52:56 -0500

The Blast Extension and Assembly Program (BEAP) is a computer program that uses a short starting DNA fragment, often a EST or partial gene segment, as "primer", to recursively blast nucleotide databases in an attempt to obtain all sequences that overlaps, directly or indirectly, with the "primer" therefore help to "extend" the length of the original sequence for constructing a "full length" sequence for functional analysis, or at least to obtain neighboring regions of the segment for SNP discovery and linkage disequilibrium analysis. The confidence of assembling the resulting sequences is achieved by using a known genome, such as human genome, as a reference. https://www.animalgenome.org/tools/beap/

Address of the bookmark: https://www.animalgenome.org/tools/beap/

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/

CrossMap: a program for convenient conversion of genome coordinates

Jit — Thu, 31 May 2018 06:00:47 -0500

CrossMap is a program for convenient conversion of genome coordinates (or annotation files) between different assemblies (such as Human hg18 (NCBI36) <> hg19 (GRCh37), Mouse mm9 (MGSCv37) <> mm10 (GRCm38)). It supports most commonly used file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF. CrossMap is designed to liftover genome coordinates between assemblies. It’s not a program for aligning sequences to reference genome. We do not recommend using CrossMap to convert genome coordinates between species.

Address of the bookmark: http://crossmap.sourceforge.net

pyGenomeTracks: Standalone program and library to plot beautiful genome browser tracks

Neel — Fri, 09 Nov 2018 12:34:23 -0600

pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable. Currently, it is possible to plot:

bigwig
bed (many options)
bedgraph
links (represented as arcs)
Hi-C matrices (if HiCExplorer is installed)

Address of the bookmark: https://github.com/deeptools/pyGenomeTracks

DISTRUCT: a program for the graphical display of population structure

Abhimanyu Singh — Mon, 25 Mar 2019 03:33:44 -0500

distruct is a program that can be used to graphically display results produced by the genetic clustering program structure or by other similar programs. The figures produced by distructdisplay individual membership coefficients in the same form as used in "Genetic structure of human populations" Science 298: 2381-2385 (2002). Various options enable the user to control left-to-right printing order of populations, bottom-to-top printing order of clusers, colors, and other graphical details. [Example]

[Download software package (includes the manual)] (you will be directed first to a registration page and we would very much appreciate if you register)
[Download manual]
[Download software note from Molecular Ecology Notes 4: 137-138 (2004)]

To use the UNIX versions, unzip and untar the files in an appropriate directory using

gunzip filename.tar.gz; tar xvf filename.tar

where "filename.tar.gz" is the downloaded file. Winzip will unzip the Windows version. Run the program by typing

./distruct

in UNIX or

distruct

from a Dos prompt in Windows. It will produce a figure using the data that are represented in the Central/South Asia K=5 plot in Science 298: 2381-2385 (2002).

Please send comments or problems with distruct to Noah Rosenberg.

October 15, 2014 — Users of Distruct may also find CLUMPP and CLUMPAK of interest.

Address of the bookmark: https://rosenberglab.stanford.edu/distruct.html

AutoDock Vina: an open-source program for doing molecular docking.

BioStar — Sat, 13 Jun 2020 07:55:56 -0500

AutoDock Vina is an open-source program for doing molecular docking. It was designed and implemented by Dr. Oleg Trott in the Molecular Graphics Lab at The Scripps Research Institute. It is especially effective for protein-ligand docking. AutoDock 4 is available under the GNU General Public License. AutoDock is one of the most cited docking software applications in the research community.

http://vina.scripps.edu/

Address of the bookmark: http://vina.scripps.edu/

BUSCO

Jitendra Narayan — Sun, 07 Feb 2016 16:02:39 -0600

Assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs

More at http://busco.ezlab.org/

Address of the bookmark: http://busco.ezlab.org/

Centurion

Jit — Fri, 12 Feb 2016 04:45:41 -0600

Although centromeres are essential for life and are the subject of extensive research, centromere locations in yeast genomes are difficult to infer, and in most species they are still unknown. Recently, the chromatin conformation assay Hi-C has been re-purposed for diverse applications, including de novo genome assembly, deconvolution of metagenomic samples, and inference of centromere locations. We describe a method, Centurion, that jointly infers the locations of all centromeres in a single yeast genome by exploiting the centromeres’ tendency to cluster in 3D space. We first demonstrate the accuracy of Centurion in identifying known centromere locations from high coverage Hi-C data of budding yeast and a human malaria parasite. We then use two metagenomic samples with relatively low coverage Hi-C data to infer centromere locations for each chromosome in 14 different yeast species. For yeasts with large centromeres (e.g., S. pombe) Centurion predicts the exact centromere locations. For seven yeasts with point centromeres, Centurion predicts most of the centromeres at an average of 5~kb distance from their known locations. Finally, we predict centromere coordinates for six yeast species that currently lack centromere annotations. These results suggest that Centurion can be used for centromere identification for a large number of yeast species, even with a limited amount of Hi-C sequencing.

Paper:http://www.ncbi.nlm.nih.gov/pubmed/25940625

More at http://cbio.ensmp.fr/centurion/

Address of the bookmark: http://cbio.ensmp.fr/centurion/

BRAKER: pipeline for fully automated prediction of protein coding genes with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes

Jit — Thu, 01 Sep 2016 08:02:59 -0500

Gene finding in eukaryotic genomes is notoriously difficult to automate. The task is to design a work flow with a minimal set of tools that would reach state-of-the-art performance across a wide range of species. GeneMark-ET is a gene prediction tool that incorporates RNA-Seq data into unsupervised training and subsequently generates ab initio gene predictions. AUGUSTUS is a gene finder that usually requires supervised training and uses information from RNA-Seq reads in the prediction step. Complementary strengths of GeneMark-ET and AUGUSTUS provided motivation for designing a new combined tool for automatic gene prediction.

http://www.ncbi.nlm.nih.gov/pubmed/26559507

Address of the bookmark: http://bioinf.uni-greifswald.de/bioinf/braker/