BOL: Related items

EAGER

Jit — Sat, 10 Dec 2016 18:07:23 -0600

The automated reconstruction of genome sequences in ancient genome analysis is a multifaceted process.

EAGER encompasses both state-of-the-art tools for each step as well as new complementary tools tailored for ancient DNA data within a single integrated solution in an easily accessible format.

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0918-z

Address of the bookmark: https://github.com/apeltzer/EAGER-GUI

DIAMOND

Jit — Thu, 27 Apr 2017 04:21:54 -0500

DIAMOND is a sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000.

More at file:///home/urbe/Downloads/diamond_manual.pdf

http://www.nature.com/nmeth/journal/v12/n1/full/nmeth.3176.html

Address of the bookmark: https://github.com/bbuchfink/diamond

SLIDESORT-BPR

Abhimanyu Singh — Mon, 20 Nov 2017 09:19:52 -0600

Chromosomal rearrangement events are caused by abnormal breaking and rejoining of DNA molecules. They are responsible for many of the cancer related diseases. Detecting the DNA breaking and repairing mechanism, therefore, may offer vital clues about the pathologic causes and diagnostic/therapeutic target of these diseases. But this effort also poses considerable challenges, because the structural variations and the genomes are different from one person to another. Intermediate comparison via reference genome could lead to the loss information. Unlike the current methods which make use the reference genome, we developed a method to detect the breakpoint reads directly from observing the differences between two (or more) NGS short reads samples. Slidesort-BPR is a command line tool implemented in C++.

Address of the bookmark: https://github.com/ewijaya/slidesort-bpr

IUPAC codes

Neel — Tue, 13 Mar 2018 05:16:05 -0500

IUPAC codes

DNA:

Nucleotide Code: Base:

---------------- -----

A.................Adenine

C.................Cytosine

G.................Guanine

T (or U)..........Thymine (or Uracil)

R.................A or G

Y.................C or T

S.................G or C

W.................A or T

K.................G or T

M.................A or C

B.................C or G or T

D.................A or G or T

H.................A or C or T

V.................A or C or G

N.................any base . or -............gap

Protein:

Amino Acid Code: Three letter Code: Amino Acid:

---------------- ------------------ -----------

A.................Ala.................Alanine

B.................Asx.................Aspartic acid or Asparagine

C.................Cys.................Cysteine

D.................Asp.................Aspartic Acid

E.................Glu.................Glutamic Acid

F.................Phe.................Phenylalanine

G.................Gly.................Glycine

H.................His.................Histidine

I.................Ile.................Isoleucine

K.................Lys.................Lysine

L.................Leu.................Leucine

M.................Met.................Methionine

N.................Asn.................Asparagine

P.................Pro.................Proline

Q.................Gln.................Glutamine

R.................Arg.................Arginine

S.................Ser.................Serine

T.................Thr.................Threonine

V.................Val.................Valine

W.................Trp.................Tryptophan

X.................Xaa.................Any amino acid

Y.................Tyr.................Tyrosine

Z.................Glx.................Glutamine or Glutamic acid

DNA Nucleotide Counter

Neel — Fri, 12 Oct 2018 04:37:01 -0500

DNA Nucleotide Counter is delivered in a DNA Baser package together with other free molecular biology tools. Download the package and double click it. The programs inside the package will be extracted to the destination folder (specified by you). Go to the destination folder and double click the program you want to use.

It installs in any computer even if you don't have administrator rights!

Address of the bookmark: http://www.dnabaser.com/download/DNA-Counter/index.html

The El-Sherif Group, Chair of Developmental Biology, Department of Biology - PhD Position

Sun, 19 Jan 2020 10:06:37 -0600

El-Sherif lab studies how genes are regulated to mediate patterning in Development. We use live and super-resolution imaging in addition to computational modeling to understand transcription dynamics at the single-cell level in three model systems: the fruit fly Drosophila melanogaster, the beetle Tribolium castaneum, and embryonic bodies derived from embryonic mouse stem cells.

In this project, you will use single-molecule techniques to label mRNA and DNA in (live and fixed) Drosophila embryos and fixed embryonic bodies. You will also use super-resolution microscopy to visualize protein condensates. Co-localization dynamics reflecting DNA-protein bindings and DNA looping events will be detected, analyzed, and used to test computational models of gene transcription.

Qualification:
MSc degree (or equivalent) in Biology, Biophysics, or Bioengineering

Experience in one or more of these areas: (1) molecular cloning, (2) imaging, (3) image analysis (using Matlab/Python/Java), (4) microfluidics, and (5) computational modeling.

How to Apply?
Send (1) your CV, (2) summary of research experience, and (3) email addresses of at least 2 references to ezzat.el-sherif@fau.de. Title your email ‘Transcription PhD Position’.

salary Grade.: E13
Total Time: 3 Jahre
Start: 01.01.2020.
End: 31.3.2020.

Address:
Dr. El-Sherif, Ezzat
Department Biologie
Professur für Zoologie (Entwicklungsbiologie) (Prof. Dr. Klingler)
Telefon 09131/85-28068, Fax 09131/85-28040, E-Mail: ezzat.el-sherif@fau.de

HNADOCK: a nucleic acid docking server for modeling RNA/DNA–RNA/DNA 3D complex structures

Poonam Mahapatra — Thu, 04 Jun 2020 23:19:07 -0500

The HNADOCK server is to predict the binding complex structure between two nucleic acid molecules through a hierarchical docking algorihtm of an FFT-based global search strategy and an intrinsic scoring function for nucleic acid interactions. Users are required to provide the three-dimensional (3D) structures of the two molecules to be docked.

Address of the bookmark: http://huanglab.phys.hust.edu.cn/hnadock/

Common methods to discover tandem repeats

BioStar — Thu, 09 Mar 2023 02:40:52 -0600

Tandem repeats are DNA sequences that are repeated in a contiguous manner in the genome. These sequences are often used as genetic markers and are important in many areas of genetics and genomics research. Here are some methods for discovering tandem repeats in genomes:

Tandem Repeat Finder: Tandem Repeat Finder is a software tool that identifies tandem repeats in DNA sequences. It is available for free download and can be used on both nucleotide and protein sequences. The tool uses a statistical algorithm to identify repeats based on their length, copy number, and overall composition.
RepeatMasker: RepeatMasker is another software tool that can identify tandem repeats in DNA sequences. It works by comparing the input sequence to a database of known repeats and then identifies any tandem repeats that match those in the database.
PCR-based methods: Polymerase chain reaction (PCR) can be used to amplify and detect tandem repeats in genomic DNA. PCR primers are designed to flank the tandem repeat region, and amplification of the target DNA fragment can be visualized on a gel. This method can be useful for detecting novel tandem repeats and for genotyping.
Southern blotting: Southern blotting is a classic method for detecting DNA fragments in a sample. It can be used to detect tandem repeats by digesting genomic DNA with a restriction enzyme, separating the fragments by gel electrophoresis, and then probing the blot with a tandem repeat-specific probe.

Overall, a combination of these methods can be used to comprehensively identify tandem repeats in genomes.

SVbyEye: R Package to visualize alignments between two or multiple DNA sequences

LEGE — Tue, 17 Sep 2024 02:34:57 -0500

R Package to visualize alignments between two or multiple DNA sequences including
a number of functionalities to facilitate processing of alignments in PAF format.

SVbyEye, an open-source R package to visualize and annotate sequence-to-sequence alignments along with various functionalities to process alignments in PAF format. The tool facilitates the characterization of complex SVs in the context of sequence homology helping resolve the mechanisms underlying their formation. Availability and implementation SVbyEye is available at https://github.com/daewoooo/SVbyEye.

Author: David Porubsky

Address of the bookmark: https://github.com/daewoooo/SVbyEye

Platypus: A Haplotype-Based Variant Caller For Next Generation Sequence Data

Shruti Paniwala — Thu, 25 Oct 2018 06:14:55 -0500

Platypus is a tool designed for efficient and accurate variant-detection in high-throughput sequencing data. By using local realignment of reads and local assembly it achieves both high sensitivity and high specificity. Platypus can detect SNPs, MNPs, short indels, replacements and (using the assembly option) deletions up to several kb. It has been extensively tested on whole-genome, exon-capture, and targeted capture data, it has been run on very large datasets as part of the Thousand Genomes and WGS500 projects, and is being used in clinical sequencing trials in the Mainstreaming Cancer Genetics programme.

Tutorial https://github.com/andyrimmer/Platypus/blob/master/misc/README.txt

Address of the bookmark: http://www.well.ox.ac.uk/platypus