<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/41493?offset=140 https://bioinformaticsonline.com/file/view/42693/dna-rna-meme Thu, 28 Jan 2021 11:23:14 -0600 https://bioinformaticsonline.com/file/view/42693/dna-rna-meme <![CDATA[DNA RNA MEME]]> Explain the DNA and RNA with picture ...

]]> Neel https://bioinformaticsonline.com/videolist/watch/2882/phylogenetics Fri, 23 Aug 2013 03:53:43 -0500 https://bioinformaticsonline.com/videolist/watch/2882/phylogenetics <![CDATA[Phylogenetics]]> 006 - Phylogenetics Paul Andersen discusses the specifics of phylogenetics. The evolutionary relationships of organisms are discovered through both morphological and molecular data. A specific type of phylogenetic tree, the cladogram, is also covered. Intro Music Atribution Title: I4dsong_loop_main.wav Artist: CosmicD Link to sound: http://www.freesound.org/people/CosmicD/sounds/72556/ Creative Commons Atribution License]]> https://bioinformaticsonline.com/researchlabs/view/40945/the-clark-lab Fri, 07 Feb 2020 13:57:24 -0600 <![CDATA[The Clark Lab]]> Study the process of Adaptive Evolution, during which species adopt novel traits to overcome challenges. We retrace the evolutionary histories of genomic elements to determine the changes underlying adaptation and to discover previously unknown genetic networks. These discoveries have already led to advances in human health, species conservation, and molecular biology.

More at http://clark.genetics.utah.edu/

]]> https://bioinformaticsonline.com/researchlabs/view/44639/the-sheppard-lab Fri, 09 Aug 2024 02:48:34 -0500 <![CDATA[The Sheppard Lab]]> Ineos Oxford Institute of Antimicrobial Research – Department of Biology – University of Oxford

Our research centres on the use of genetics/genomics and phenotypic studies to address complex questions in the ecology, epidemiology and evolution of microbes. Our most recent interest focuses upon comparative genome analysis to describe the core and flexible genome of pathogenic bacteria (Campylobacter, Acinetobacter, Escherichia coli, Helicobacter, Staphylococcus and Streptococcus suis) and how this is related to population genetic structuring, the maintenance of species, and the evolution of host/niche adaptation and virulence.

More at https://sheppardlab.com/research/

]]> https://bioinformaticsonline.com/blog/view/44775/genomic-architecture-surrounding-the-fusion-site-of-human-chromosome-2 Tue, 04 Mar 2025 12:26:29 -0600 https://bioinformaticsonline.com/blog/view/44775/genomic-architecture-surrounding-the-fusion-site-of-human-chromosome-2 <![CDATA[Genomic architecture surrounding the fusion site of human chromosome 2]]> The article "Genomic Structure and Evolution of the Ancestral Chromosome Fusion Site in 2q13–2q14.1 and Paralogous Regions on Other Human Chromosomes (https://pmc.ncbi.nlm.nih.gov/articles/PMC187548/)" explores the genomic architecture surrounding the fusion site of human chromosome 2. This fusion event is a key evolutionary marker distinguishing humans from other great apes, as humans have 46 chromosomes while chimpanzees, gorillas, and orangutans possess 48. The fusion occurred through an end-to-end joining of two ancestral chromosomes, which remain separate in nonhuman primates.

Key Findings:

  1. Chromosomal Fusion and Its Molecular Signature:

    • The fusion site is located at 2q13–2q14.1 and is characterized by degenerate telomeric sequences appearing interstitially, indicating the historical head-to-head joining of ancestral chromosomes.
    • Despite being a signature of a past fusion event, these telomeric repeats are no longer functional and have undergone sequence degradation over time.

  2. Extensive Duplications in the Surrounding Genomic Region:

    • The study identifies large-scale segmental duplications flanking the fusion site, with several of these regions duplicated and scattered across multiple chromosomes.
    • These duplications are predominantly located in subtelomeric and pericentromeric regions, suggesting their role in genomic instability and chromosomal evolution.

  3. Paralogous Regions and Their Evolutionary Relationships:

    • A 168-kilobase (kb) segment near the fusion site has 98%–99% sequence identity with three regions on chromosome 9 (9pter, 9p11.2, and 9q13).
    • Another 67-kb region distal to the fusion site shows a high degree of homology to sequences in chromosome 22qter.
    • Additionally, a 100-kb segment exhibits 96% sequence identity with a region in chromosome 2q11.2.

  4. Comparative Genomics and Evolutionary Implications:

    • By comparing the duplicated sequences and their arrangement in primates, the researchers traced the order of duplication events leading to their present distribution.
    • The presence of specific repetitive elements within these duplicated segments serves as evolutionary markers that help infer their historical rearrangements.
    • Some of these duplicated regions are associated with chromosomal inversion breakpoints, potentially contributing to evolutionary changes in primates.
    • Recurrent structural rearrangements in these regions have been linked to human chromosomal disorders.

Conclusions and Implications:

  • The findings provide valuable insights into the structural evolution of human chromosome 2, which played a crucial role in human speciation.
  • Understanding these segmental duplications and their evolutionary trajectories sheds light on genomic instability, which may contribute to human genetic diseases.
  • The study highlights how large-scale chromosomal rearrangements, such as fusion and duplication, have influenced the evolutionary divergence of humans from other primates.

This research advances our understanding of human genome evolution and offers a foundation for studying the effects of structural variants in genetic disorders.

]]> LEGE https://bioinformaticsonline.com/researchlabs/view/45297/comparative-genomics-of-gene-expression-lab Wed, 09 Sep 2026 03:35:46 -0500 <![CDATA[Comparative genomics of gene expression lab]]> The core expertise of the lab is comparative genomics. We combine evolutionary bioinformatics and molecular biology to understand the mechanism, function and evolution of genes.
We study the processes of gene expression and protein synthesis, and we are particularly interested in the phenomenon of translational recoding (programmed exceptions to the genetic code). For more information, see Research.

More at https://www.mariottigenomicslab.com/

]]> https://bioinformaticsonline.com/bookmarks/view/37584/mulan-multiple-sequence-local-alignment-and-visualization-for-studying-function-and-evolution Fri, 24 Aug 2018 09:50:01 -0500 https://bioinformaticsonline.com/bookmarks/view/37584/mulan-multiple-sequence-local-alignment-and-visualization-for-studying-function-and-evolution <![CDATA[Mulan: Multiple-sequence local alignment and visualization for studying function and evolution]]> Mulan: Multiple-sequence local alignment and visualization for studying function and evolution

Mulan (http://mulan.dcode.org/), a novel method and a network server for comparing multiple draft and finished-quality sequences to identify functional elements conserved over evolutionary time. Mulan brings together several novel algorithms: the TBA multi-aligner program for rapid identification of local sequence conservation, and the multiTF program for detecting evolutionarily conserved transcription factor binding sites in multiple alignments. In addition, Mulan supports two-way communication with the GALA database; alignments of multiple species dynamically generated in GALA can be viewed in Mulan, and conserved transcription factor binding sites identified with Mulan/multiTF can be integrated and overlaid with extensive genome annotation data using GALA.

Address of the bookmark: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC540288/

]]> Jit https://bioinformaticsonline.com/researchlabs/view/39704/the-rogers-lab Mon, 15 Jul 2019 08:07:44 -0500 <![CDATA[The Rogers Lab]]> The Rogers lab studies evolution of genome structure. We explore the ways that complex mutations like duplications, deletions, rearrangements, and retrogenes can create new genetic material. We study how these new mutations are important for adaptation. We are currently working on projects in Drosophila, Mammoths, Elephants, Bivalves, and Frogs absolutely no amphibians. This multi-organism approach can help us understand when and why complex mutations are important for organism fitness.

More at http://evolscientist.com/

]]> https://bioinformaticsonline.com/bookmarks/view/37650/p-rna-scaffolder-a-fast-and-accurate-genome-scaffolder-using-paired-end-rna-sequencing-reads Fri, 07 Sep 2018 05:19:06 -0500 https://bioinformaticsonline.com/bookmarks/view/37650/p-rna-scaffolder-a-fast-and-accurate-genome-scaffolder-using-paired-end-rna-sequencing-reads <![CDATA[P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads]]> P_RNA_scaffolder is a novel scaffolding tool using Pair-end RNA-seq to scaffold genome fragments. The method is suitable for most genomes. The program could utilize Illumina Paired-end RNA-sequencing reads from target speciesies. Our method provides another practical alternative to existing mate-pair_based approaches or other Protein-based approaches (for instance, PEP_scaffolder ) for scaffolding genome sequences. The most important feature of this method is to improve the completeness of gene regions and long-coding gene regions (for instance, circRNA).

Address of the bookmark: http://www.fishbrowser.org/software/P_RNA_scaffolder/#

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/38670/ltr-finder-an-efficient-program-for-finding-full-length-ltr-retrotranspsons-in-genome-sequences Sun, 13 Jan 2019 07:05:53 -0600 https://bioinformaticsonline.com/bookmarks/view/38670/ltr-finder-an-efficient-program-for-finding-full-length-ltr-retrotranspsons-in-genome-sequences <![CDATA[LTR_Finder: an efficient program for finding full-length LTR retrotranspsons in genome sequences.]]> LTR_Finder is an efficient program for finding full-length LTR retrotranspsons in genome sequences.

The Program first constructs all exact match pairs by a suffix-array based algorithm and extends them to long highly similar pairs. Then Smith-Waterman algorithm is used to adjust the ends of LTR pair candidates to get alignment boundaries. These boundaries are subject to re-adjustment using supporting information of TG..CA box and TSRs and reliable LTRs are selected. Next, LTR_FINDER tries to identify PBS, PPT and RT inside LTR pairs by build-in aligning and counting modules. RT identification includes a dynamic programming to process frame shift. For other protein domains, LTR_FINDER calls ps_scan (from PROSITE, http://www.expasy.org/prosite/) to locate cores of important enzymes if they occur.

Address of the bookmark: https://github.com/xzhub/LTR_Finder

]]> Neel