Browsing by Author "Bilgin, Halil İbrahim"

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    ConVarT: A search engine for matching human genetic variants with variants from non-human species
    (Oxford University Press, 2022) Pir, Mustafa; Bilgin, Halil I.; Sayıcı, Ahmet; Coşkun, Fatih; Torun, Furkan M; Zhao, Pei; Kang, Yahong; Çevik, Sebiha; Kaplan, Oktay İsmail; 0000-0002-8733-0920; 0000-0002-0935-1929; AGÜ, Mühendislik Fakültesi, Bilgisayar Mühendisliği Bölümü; Pİr, Mustafa; Bilgin, Halil İbrahim; Sayıcı, Ahmet; Coşkun, Fatih; Torun, Furkan M.; Çevik, Sebiha; Kaplan, Oktay İsmail
    The availability of genetic variants, together with phenotypic annotations from model organisms, facilitates comparing these variants with equivalent variants in humans. However, existing databases and search tools do not make it easy to scan for equivalent variants, namely 'matching variants' (MatchVars) between humans and other organisms. Therefore, we developed an integrated search engine called ConVarT (http://www.convart.org/) for matching variants between humans, mice, and Caenorhabditis elegans. ConVarT incorporates annotations (including phenotypic and pathogenic) into variants, and these previously unexploited phenotypic MatchVars from mice and C. elegans can give clues about the functional consequence of human genetic variants. Our analysis shows that many phenotypic variants in different genes from mice and C. elegans, so far, have no counterparts in humans, and thus, can be useful resources when evaluating a relationship between a new human mutation and a disease.
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    MSABrowser: dynamic and fast visualization of sequence alignments, variations and annotations
    (Oxford University Press, 2021) Torun, Furkan M.; Bilgin, Halil İbrahim; Kaplan, Oktay I.; AGÜ, Mühendislik Fakültesi, Bilgisayar Mühendisliği Bölümü; Bilgin, Halil İbrahim; Torun, Furkan M.; Kaplan, Oktay I.
    Sequence alignment is an excellent way to visualize the similarities and differences between DNA, RNA or protein sequences, yet it is currently difficult to jointly view sequence alignment data with genetic variations, modifications such as post-translational modifications and annotations (i.e. protein domains). Here, we present the MSABrowser tool that makes it easy to co-visualize genetic variations, modifications and annotations on the respective positions of amino acids or nucleotides in pairwise or multiple sequence alignments. MSABrowser is developed entirely in JavaScript and works on any modern web browser at any platform, including Linux, Mac OS X and Windows systems without any installation. MSABrowser is also freely available for the benefit of the scientific community.