BOL: Related items

Doctoral student (m / w / d) - mucosal immunology (Imaging)

Mon, 24 Jun 2019 22:27:25 -0500

Since its founding in 1815, the University Hospital Erlangen has been offering top-quality medicine. In diagnosis and therapy are the latest findings of medical research. More than 7500 employees from around 50 professions are needed to fulfill the manifold tasks of the University Hospital Erlangen.
tasks
The research goal is the analysis of the role of Itk (Tec Kinase) in chronic intestinal inflammation. The focus of the planned work is on immunological work such as cell culture, FACS, ELISA, qPCR analysis of clinical samples. The project is funded by third party funds and already established as part of a SFB project.
qualifications
Doctoral student (m / w / d) in the research field "Immunology of the Gastrointestinal tract".
-Degree in Natural Sciences (MSc or equivalent)
-Excellent Study
Skills -Found knowledge and skills of molecular biological, immunological and microscopy
techniques -Very good knowledge of English
-team
skills -responsibility, self-initiative, motivation and purposefulness would

also be beneficial:
-Experience in imaging
methods -experience desirable in cell culture, FACS, histochemistry
We offer
A safe, interesting job in a motivated open-minded research team. Careful and skilled training and support in the new challenge. A varied and responsible field of activity with individual development opportunities.
Comprehensive offers for health promotion
All services of the civil service incl. Additional provision of the Federal
and Länder pension funds (VBL)
Family-friendly environment and, where applicable, dormitory
places Crediting of professional experience possible
Contact for applications
Applications with curriculum vitae, certificates and letters of recommendation can preferably be sent by mail or postal mail to:

PD Dr. med. rer. nat. Dr. habil. med. Weigmann, Benno
University Hospital Erlangen
Medical Clinic 1 - Research
Hartmannstraße 14
91054 Erlangen
09131-8535885

https://www.jobvector.de/en/jobs/biology-life-sciences/research-education/naturwissenschaftlicher-doktorand-mukosale-immunologie-120008.html?suid=62e3e74c0250f5577074cb7c9fa0c2e655323ac8

Strudel

Anjana — Fri, 30 Sep 2016 09:47:02 -0500

Strudel is our graphical tool for visualizing genetic and physical maps of genomes for comparative purposes. The application aims to let the user examine their data at a variety of different levels of resolution, from entire maps to individual markers, and explore syntenic relationships between genomes. All browsing and interaction with Strudel happens in real-time – there is no need to wait while the maps are generated. It is built using Java 1.6 and ships with its own JRE, so there is no need for users to install or update Java.

Address of the bookmark: https://ics.hutton.ac.uk/strudel/

Gene Synteny Database

Jit — Fri, 16 Dec 2016 11:09:39 -0600

Comparative genomics remains a pivotal strategy to study the evolution of gene organization, and this primacy is reinforced by the growing number of full genome sequences available in public repositories. Despite this growth, bioinformatic tools available to visualize and compare genomes and to infer evolutionary events remain restricted to two or three genomes at a time, thus limiting the breadth and the nature of the question that can be investigated. Here we present Genomicus, a new synteny browser that can represent and compare unlimited numbers of genomes in a broad phylogenetic view. In addition, Genomicus includes reconstructed ancestral gene organization, thus greatly facilitating the interpretation of the data.

Availability: Genomicus is freely available for online use at http://www.dyogen.ens.fr/genomicus while data can be downloaded at ftp://ftp.biologie.ens.fr/pub/dyogen/genomicus

Contact: rf.sne.eigoloib@crh

Address of the bookmark: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2853686/

Synteny and Rearrangement Identifier (SyRI)

Jit — Tue, 05 May 2020 10:37:10 -0500

SyRI is a comprehensive tool for predicting genomic differences between related genomes using whole-genome assemblies (WGA). The assemblies are aligned using whole-genome alignment tools, and these alignments are then used as input to SyRI. SyRI identifies syntenic path (longest set of co-linear regions), structural rearrangements (inversions, translocations, and duplications), local variations (SNPs, indels, CNVs etc) within syntenic and structural rearrangements, and un-aligned regions.

Address of the bookmark: https://schneebergerlab.github.io/syri/

xmatchview: smith-waterman alignment visualization

Rahul Nayak — Thu, 28 Dec 2017 09:00:58 -0600

xmatchview and xmatchview-conifer are imaging tools for comparing the synteny between DNA sequences. It allows users to align 2 DNA sequences in fasta format using cross_match and displays the alignment in a variety of image formats. xmatchview and xmatchview-conifer are written in python and run on linux and windows. They serve as visual tools for analyzing cross_match alignments. Cross_match (Green, P. (1994) http://www.phrap.org) uses an implementation of the Smith-Waterman algorithm for comparing DNA sequences that is sensitive.

http://www.bcgsc.ca/platform/bioinfo/software/xmatchview

Address of the bookmark: https://github.com/warrenlr/xmatchview

flexidot: Highly customizable, ambiguity-aware dotplots for visual sequence analyses

Jit — Fri, 24 Apr 2020 08:39:28 -0500

FlexiDot is a cross-platform dotplot suite generating high quality self, pairwise and all-against-all visualizations. To improve dotplot suitability for comparison of consensus and error-prone sequences, FlexiDot harbors routines for strict and relaxed handling of mismatches and ambiguous residues. The custom shading modules facilitate dotplot interpretation and motif identification by adding information on sequence annotations and sequence similarities to the images. Combined with collage-like outputs, FlexiDot supports simultaneous visual screening of a large sequence sets, allowing dotplot use for routine screening.

Address of the bookmark: https://github.com/molbio-dresden/flexidot

JCVI utility libraries

Jit — Sat, 08 May 2021 22:04:02 -0500

Collection of Python libraries to parse bioinformatics files, or perform computation related to assembly, annotation, and comparative genomics.

Address of the bookmark: https://github.com/tanghaibao/jcvi

Scalpel

Shruti Paniwala — Wed, 20 Aug 2014 02:07:58 -0500

A team from Cold Spring Harbor Laboratory has released an algorithm, called Scalpel, for finding insertions and deletions in next generation sequencing data sets. Scalpel, which is open source and available for download on SourceForge, outperformed the popular tools GATK HaplotypeCaller and SOAPindel in test runs on both simulated and real whole human exomes.

Like other indel callers, Scalpel works by performing de novo assembly of regions of interest, so that misalignment to the reference genome cannot obscure the presence of an insertion or deletion. Scalpel's innovation is to repeatedly check its assembly before comparing to the reference genome, to account for simple sequence repeats that are a regular source of error in indel calling. When Scalpel assembles an exon, it collects reads that map to that exon (including partial matches), splits them into k-mers, and creates a de Bruijn graph to span the exon; however, if it detects repeats in the map, it iteratively increases the size of the k-mers by one base until the repeats are eliminated. This ensures that the final assembly of the exon is highly accurate while minimizing compute time.

The Cold Spring Harbor team's validation of Scalpel, published over the weekend in Nature Methods, compares Scalpel's performance on a live whole exome against HaplotypeCaller and SOAPindel. The donor is an individual with serious neurological disorders, which may be linked to a high incidence of indels. One thousand indels from this individual's exome, called by one or more of the informatics pipelines, were selected for focused resequencing. This resequencing revealed a 77% true positive rate for Scalpel calls, dramatically better than the rates for either of the competing tools; Scalpel performed especially well with indels longer than five base pairs, a traditional weak point for indel callers.

Finally, the authors demonstrate Scalpel's use on a large set of genetic data from nearly 600 families who donated samples to the Simons Simplex Collection, a project of the Simons Foundation Autism Research Initiative. Scalpel found a very high enrichment for indels in children affected by autism, compared with their unaffected siblings, a pattern that persisted even after excluding common variants.

Picard

Neel — Fri, 29 Apr 2016 08:21:54 -0500

Picard is a set of command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. These file formats are defined in the Hts-specs repository. See especially the SAM specification and the VCF specification.

Note that the information on this page is targeted at end-users. For developers, the source code, building instructions and implementation/development resources are available on GitHub.

The Picard toolkit is open-source under the MIT license and free for all uses.

Enjoy!

Address of the bookmark: http://broadinstitute.github.io/picard/

Andi

Jit — Fri, 13 May 2016 05:16:35 -0500

This is the andi program for estimating the evolutionary distance between closely related genomes. These distances can be used to rapidly infer phylogenies for big sets of genomes. Because andi does not compute full alignments, it is so efficient that it scales even up to thousands of bacterial genomes.

This readme covers all necessary instructions for the impatient to get andi up and running. For extensive instructions please consult the manual.

More at https://github.com/evolbioinf/andi/

Address of the bookmark: http://bioinformatics.oxfordjournals.org/content/early/2015/01/13/bioinformatics.btu815.full