<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/4943?offset=290 https://bioinformaticsonline.com/bookmarks/view/36456/alpaca-a-hybrid-strategy-for-assembly-of-genomic-dna-shotgun-sequencing-reads Mon, 30 Apr 2018 04:38:40 -0500 https://bioinformaticsonline.com/bookmarks/view/36456/alpaca-a-hybrid-strategy-for-assembly-of-genomic-dna-shotgun-sequencing-reads <![CDATA[ALPACA: A hybrid strategy for assembly of genomic DNA shotgun sequencing reads.]]> ALPACA requires Celera Assembler 8.3 or later. It is recommended to build Celera Assembler from source. (Why? The pre-built binaries CA_8.3rc1 and CA8.3rc2 will work for any large data set. 

Detail paper at https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-3927-8

Address of the bookmark: https://github.com/VicugnaPacos/ALPACA

]]> Seema Singh https://bioinformaticsonline.com/bookmarks/view/37915/dna-nucleotide-counter Fri, 12 Oct 2018 04:37:01 -0500 https://bioinformaticsonline.com/bookmarks/view/37915/dna-nucleotide-counter <![CDATA[DNA Nucleotide Counter]]> 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

]]> Neel https://bioinformaticsonline.com/opportunity/view/40566/the-el-sherif-group-chair-of-developmental-biology-department-of-biology-phd-position Sun, 19 Jan 2020 10:06:37 -0600 <![CDATA[The El-Sherif Group, Chair of Developmental Biology, Department of Biology - PhD Position]]> 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

]]> https://bioinformaticsonline.com/bookmarks/view/41602/nucdiff-in-depth-characterization-and-annotation-of-differences-between-two-sets-of-dna-sequences Tue, 05 May 2020 10:35:48 -0500 https://bioinformaticsonline.com/bookmarks/view/41602/nucdiff-in-depth-characterization-and-annotation-of-differences-between-two-sets-of-dna-sequences <![CDATA[NucDiff: In-depth characterization and annotation of differences between two sets of DNA sequences]]> NucDiff locates and categorizes differences between two closely related nucleotide sequences. It is able to deal with very fragmented genomes, structural rearrangements and various local differences. These features make NucDiff to be perfectly suitable to compare assemblies with each other or with available reference genomes.

NucDiff provides information about the types of differences and their locations. It is possible to upload the results into genome browser for visualization and further inspection. It was written in Python and uses the NUCmer package from MUMmer[1] for sequence comparison.



Address of the bookmark: https://github.com/uio-cels/NucDiff

]]> Jit https://bioinformaticsonline.com/bookmarks/view/43268/kmer-a-suite-of-tools-for-dna-sequence-analysis Wed, 18 Aug 2021 00:02:54 -0500 https://bioinformaticsonline.com/bookmarks/view/43268/kmer-a-suite-of-tools-for-dna-sequence-analysis <![CDATA[Kmer: a suite of tools for DNA sequence analysis]]> More at https://help.rc.ufl.edu/doc/Kmer

This also includes:

  • A2Amapper: ATAC, Assembly to Assembly Comparision tool:
    • Comparative mapping between two genome assemblies (same species), or between two different genomes (cross species).
  • Sim4db:
    • Spliced alignment of cDNA and genomic sequences, from the same (sim4) or related (sim4cc) species. Optimized for high-throughput batched alignment.
  • LEAFF:
    • LEAFF (ahem, Let's Extract Anything From Fasta) is a utility program for working with multi-fasta files. In addition to providing random access to the base level, it includes several analysis functions.
  • Meryl:
    • An out-of-core k-mer counter. The amount of sequence that can be processed for any size k depends only on the amount of free disk space.

Address of the bookmark: https://help.rc.ufl.edu/doc/Kmer

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/44559/metagraph-ultra-scalable-framework-for-dna-search-alignment-assembly Sat, 08 Jun 2024 16:15:25 -0500 https://bioinformaticsonline.com/bookmarks/view/44559/metagraph-ultra-scalable-framework-for-dna-search-alignment-assembly <![CDATA[MetaGraph: Ultra Scalable Framework for DNA Search, Alignment, Assembly]]> The MetaGraph framework is designed to work with a wide range of input data sets, indexing from a few samples up to the contents of entire archives with hundreds of thousands of records. The indexing workflow always follows the same principle, transforming single input samples into error-removed, refined sample graphs, which are then merged into a joint metagraph index. Each input sample is annotated in the joint index as a subgraph. This graph index enriched with metadata can then be used for downstream applications such as sequence search or differential assembly.

Searcg link https://metagraph.ethz.ch/search 

Pre-print https://www.biorxiv.org/content/10.1101/2020.10.01.322164v4 

Address of the bookmark: https://metagraph.ethz.ch/

]]> Abhi https://bioinformaticsonline.com/bookmarks/view/40994/biological-databases Wed, 12 Feb 2020 01:16:29 -0600 https://bioinformaticsonline.com/bookmarks/view/40994/biological-databases <![CDATA[Biological databases !]]> Now a days there are a lots of genomics databases available around the world. This bookmark is created to provide all links in one place ...

ftp://ftp.ncbi.nih.gov/genomes/

https://hgdownload.soe.ucsc.edu/downloads.html

Address of the bookmark: ftp://ftp.ncbi.nih.gov/genomes/

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/5350/introduction-of-epigenomics Sun, 06 Oct 2013 04:59:30 -0500 https://bioinformaticsonline.com/bookmarks/view/5350/introduction-of-epigenomics <![CDATA[Introduction of Epigenomics]]>
  • What is the epigenome?
  • What does the epigenome do?
  • What makes up the epigenome?
  • Is the epigenome inherited?
  • What is imprinting?
  • Can the epigenome change?
  • What makes the epigenome change?
  • How do changes in the epigenome contribute to cancer?
  • How are researchers exploring the epigenome?

    • Address of the bookmark: http://www.genome.gov/27532724

    ]]>     Rahul Agarwal     https://bioinformaticsonline.com/researchlabs/view/40881/liu-lab Tue, 04 Feb 2020 06:27:02 -0600 <![CDATA[Liu Lab]]> Shirley is a computational biologist with expertise in cancer epigenetics. Her research focuses on algorithm development and integrative mining from big data generated on microarrays, massively parallel sequencing, and other high throughput techniques to model the specificity and function of transcription factors, chromatin regulators and lncRNAs in tumor development, progression, drug response and resistance.

    https://liulab-dfci.github.io/software/

    ]]>         https://bioinformaticsonline.com/bookmarks/view/23251/directional-dominance-on-stature-and-cognition-in-diverse-human-populations Sat, 11 Jul 2015 12:43:51 -0500 https://bioinformaticsonline.com/bookmarks/view/23251/directional-dominance-on-stature-and-cognition-in-diverse-human-populations <![CDATA[Directional dominance on stature and cognition in diverse human populations]]> Analysis of the genomes of >350,000 individuals revealed the existence of a small though measureable association between genome-wide homozygosity and some vital complex traits...

    Directional dominance is predicted for traits under directional evolutionary selection, this study provides evidence that increased stature and cognitive function have been positively selected in human evolution, whereas many important risk factors for late-onset complex diseases may not have been.

    http://www.nature.com/nature/journal/vaop/ncurrent/full/nature14618.html

    Address of the bookmark: http://www.nature.com/nature/journal/vaop/ncurrent/full/nature14618.html

    ]]>     Rahul Agarwal