Contact:
Computer Science Building (Science Park 3)
Altenberger Str. 69, A-4040 Linz, Austria
Tel. +43 732 2468 4520 / Fax +43 732 2468 4539
E-mail secretary@bioinf.jku.at

http://www.bioinf.jku.at/

RaGOO is a tool for coalescing genome assembly contigs into pseudochromosomes via minimap2 alignments to a closely related reference genome. The focus of this tool is on practicality and therefore has the following features:

1. Good performance. On a MacBook Pro using Arabidopsis data, pseudochromosome construction takes less than a minute and the whole pipeline with SV calling takes ~2 minutes.
2. Intact ordering and orienting of contigs.
3. Chimeric contig correction
4. GFF lift-over
5. Structural variant calling with and integrated version of Assemblytics
6. Confidence scores associated with the grouping, localization, and orientation for each contig.

Address of the bookmark: https://github.com/malonge/RaGOO

What Are lncRNAs?

lncRNAs are RNA transcripts longer than 200 nucleotides that do not code for proteins. Despite their non-coding nature, they play diverse roles in gene regulation, including chromatin remodeling, transcriptional control, and post-transcriptional processing. Unlike messenger RNAs (mRNAs), lncRNAs often function as scaffolds, decoys, or guides in cellular machinery, influencing biological processes such as cell differentiation, immune response, and even cancer metastasis.

Challenges in lncRNA Research

Identifying and understanding lncRNAs pose unique challenges:

1. High Sequence Variability: Unlike protein-coding genes, lncRNAs exhibit low sequence conservation across species, making functional predictions difficult.
2. Low Expression Levels: lncRNAs are often expressed at low levels, complicating their detection in transcriptomic data.
3. Diverse Functions: The multifunctional nature of lncRNAs requires advanced computational tools to decipher their roles in complex networks.

Bioinformatics: A Crucial Ally in lncRNA Research

Bioinformatics bridges the gap between raw biological data and meaningful insights, making it indispensable in lncRNA research. Here’s how:

1. Identification and Annotation

High-throughput sequencing technologies like RNA-seq generate vast amounts of data. Bioinformatics tools such as StringTie, Cufflinks, and HISAT2 help assemble and annotate lncRNAs from this data. Additionally, databases like NONCODE, LNCipedia, and Ensembl provide curated repositories of lncRNA sequences and annotations.

2. Functional Prediction

Bioinformatics algorithms predict the potential functions of lncRNAs by analyzing their interactions with DNA, RNA, and proteins. Tools like LncRNA2Function and RIblast utilize sequence motifs and secondary structure predictions to hypothesize about the roles of specific lncRNAs.

3. Network Construction

lncRNAs often act as regulatory hubs. Bioinformatics platforms such as Cytoscape enable the visualization of lncRNA-mediated networks, elucidating their roles in pathways like cell cycle regulation and apoptosis.

4. Epigenetic Studies

lncRNAs are known to interact with chromatin-modifying complexes, influencing gene expression epigenetically. Tools like ChIP-seq and ATAC-seq, combined with computational pipelines, identify these interactions and map them to the genome.

5. Clinical Applications

Bioinformatics aids in the discovery of lncRNA biomarkers for diseases like cancer and neurodegenerative disorders. Machine learning models analyze differential expression profiles, helping prioritize lncRNAs with therapeutic potential.

Case Study: lncRNAs in Cancer Research

lncRNAs such as HOTAIR and MALAT1 have been implicated in cancer progression. Bioinformatics analyses have revealed their roles in promoting metastasis and altering the tumor microenvironment. For example, transcriptome analysis in cancer patients identifies lncRNA expression signatures, enabling precision medicine approaches.

Future Directions

The fusion of bioinformatics with experimental biology is unlocking the secrets of lncRNAs. Advances in artificial intelligence, single-cell sequencing, and structural modeling promise to overcome current limitations. Here are some promising directions:

• Integrative Analysis: Combining multi-omics data to understand the interplay of lncRNAs with other biomolecules.
• CRISPR Screens: Leveraging bioinformatics to design CRISPR-based functional screens for lncRNAs.
• Therapeutic Development: Using bioinformatics to design lncRNA-based therapeutics, including antisense oligonucleotides and RNA interference tools.

Conclusion

lncRNAs are the hidden gems of the genome, and bioinformatics is the key to unearthing their full potential. As research progresses, lncRNAs could pave the way for novel diagnostics, targeted therapies, and personalized medicine, revolutionizing our approach to complex diseases.

The journey into the world of lncRNAs is only beginning, and bioinformatics will continue to play a pivotal role in decoding these molecular mysteries. Whether you’re a researcher, clinician, or bioinformatics enthusiast, the study of lncRNAs offers a fascinating frontier of discovery.

Mitofinder is a pipeline to assemble mitochondrial genomes and annotate mitochondrial genes from trimmed read sequencing data.

MitoFinder is also designed to find and annotate mitochondrial sequences in existing genomic assemblies (generated from Hifi/PacBio/Nanopore/Illumina sequencing data...)

MitoFinder is distributed under the license.

Address of the bookmark: https://github.com/RemiAllio/MitoFinder

Address of the bookmark: https://github.com/cschin/Peregrine

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

The software is implemented in Python 3 and runs in both Python 2.7 and 3.4– on Macintosh and Linux systems. It is freely available at https://github.com/nigyta/dfast_core/ under the GPLv3 license with external binaries bundled in the software distribution. An on-line version is also available at https://dfast.nig.ac.jp/.

Address of the bookmark: https://dfast.nig.ac.jp/

We first operate a rapid inspection of the different BAM files using samtools flagstat. Illumina provided chr21 read mapping obtained with their GA IIx deep sequencing platform <ftp://webdata:webdata@ussd-ftp.illumina.com/Data/SequencingRuns/NA18507_GAIIx_100_chr21.bam>, aligned to the b36/hg18 reference genome)

Address of the bookmark: https://wiki.bits.vib.be/index.php/NGS_Exercise.6#compare_aln_.26_mem_results_with_vcf-compare

This is a fixed term post for 36 months.

We wish to recruit a highly motivated, postdoctoral scientist to carry out a BBSRC funded project in the laboratory of Dr. Denis Larkin. The project is focused on developing and applying new algorithms to study genome and chromosome evolution in birds, mammals and other vertebrate species using whole-genome sequences and existing algorithms. The post holder will use cutting edge computational and laboratory approaches to generate chromosomal assemblies for sequenced genomes, study chromosomal structures and genome differences between bird and other vertebrate species in attempt to identify species- and clade-specific genome signatures.

Applicants must have a Ph.D. and a track record of success, as indicated by first-author publications in international journals. They must possess excellent organisation skills and be capable of individual initiative and of interacting as part of a team. Applicants with extensive practical experience in bioinformatics or computer science, programming, visualization, handling of large data sets, high-performance computing are encouraged to apply. The post will involve collaboration with a wide range of academic partners both within the UK, EU and worldwide. In addition to leading their own project the post holder will have opportunities to contribute to multiple international genome initiatives.

Experience in programming, bioinformatics and comparative genome analysis is essential. Applicants should have a minimum of a degree and preferably a higher degree in a relevant subject.

The Royal Veterinary College has the largest range of veterinary, para-veterinary and animal science undergraduate and postgraduate courses of any veterinary school in the world and is one of the largest veterinary schools in Europe.

Prospective applicants are encouraged to contact Dr. Denis Larkin, Comparative Biomedical Sciences Department on +442071211906 or email: dlarkin@rvc.ac.uk

We offer a generous reward package.

For further information and to apply on-line please visit our website: www.rvc.ac.uk
Job reference CBS-0025-14A

Closing date: 4 July 2014
Interviews are likely to be held in July 2014

We promote equality of opportunity and diversity within the workplace and welcome applications from all sections of the community.