Genes and Genomes The OSDD OpenLab has been maintaining the OSDD Open Access Repository of clinical isolates of Mycobacterium tuberculosis. A number of isolates from this repository has been sequenced and available in public domain. A number of genomes from the OSDD Open Access Repository has been sequenced in Dr. Sridhar Sivasubbu Laboratory in collaboration. A complete list of the sequenced strains and publications are available here. TBvar Resource for Genomic Variations tbvar is a comprehensive resource for genomic variations in Mycobacterium tuberculosis The variations have been systematically retrieved from high-throughput re-sequencing data-sets. In addition, Using a systematic computational pipeline, potential genomic variations with functional consequences and association with drug resistance have been characterized. Access this resource at URL: http://genome.igib.res.in/tbvar Joshi KR, Dhiman H, Scaria V* tbvar: a comprehensive genome variation resource for Mycobacterium tuberculosis Database (2014) 2014: bat083. Funding and Support We acknowledge the funding from the Open Source Drug Discovery Initiative/ CSIR for the programme. We also acknowledge the availability of communication and compute resources from NKN for the project. | Publications Periwal V, Patowary A, Vellarikkal SK, Gupta A, Singh M, Mittal A, Jeyapaul S, Chauhan RK, Singh AV, Singh PK, Garg P, Katoch VM, Katoch, K, OSDD Consortium, Chauhan DS*, Sivasubbu S*, Scaria V* Comparative Whole-Genome Analysis of Clinical Isolates Reveals Characteristic Architecture of Mycobacterium tuberculosis Pangenome PLoS ONE (2015) Apr 8;10(4):e0122979. doi: 10.1371/journal.pone.0122979. eCollection 2015. Sahajpal R, Kandoi G, Dhiman H, Raj S, OSDD Consortium, Scaria V, Bhartiya D and Hasija Y HGV&TB: A comprehensive online resource on Human genes and genetic variants associated with Tuberculosis Database (2014) Dec 13;2014:bau112. doi: 10.1093/database/bau112. Joshi KR, Dhiman H, Scaria V* tbvar: a comprehensive genome variation resource for Mycobacterium tuberculosis Database (2014) 2014: bat083. Vellarikkal SK, Singh AV, Singh PK, Garg P, Katoch VM, Katoch K; Open Source Drug Discovery Consortium, Chauhan DS, Sivasubbu S, Scaria V. Draft Genome Sequence of a Multidrug-Resistant Clinical Isolate of Mycobacterium tuberculosis Belonging to a Novel Spoligotype. Genome Announc. 2013 Nov 21;1(6). pii: e00965-13. doi: 10.1128/genomeA.00965-13. Vellarikkal SK, Singh AV, Singh PK, Garg P, Katoch VM, Katoch K; Open Source Drug Discovery Consortium, Chauhan DS, Sivasubbu S, Scaria V. Draft Genome Sequence of Multidrug-Resistant Mycobacterium tuberculosis Clinical Isolate OSDD515, Belonging to the Uganda I Genotype. Genome Announc. 2013 Nov 21;1(6). pii: e00750-13. doi: 10.1128/genomeA.00750-13. Karuthedath Vellarikkal S, Vir Singh A, Kumar Singh P, Garg P, Mohan Katoch V, Katoch K; Open Source Drug Discovery Consortium, Chauhan DS, Scaria V, Sivasubbu S. Draft Genome Sequence of an Extensively Drug-Resistant Mycobacterium tuberculosis Clinical Isolate of the Ural Strain OSDD493. Genome Announc. 2013 Nov 7;1(6). pii: e00928-13. doi: 10.1128/genomeA.00928-13. Karuthedath Vellarikkal S, Patowary A, Singh M, Periwal V, Singh AV, Singh PK, Garg P, Mohan Katoch V, Katoch K, Jangir PK, Sharma R; Open Source Drug Discovery Consortium, Chauhan DS, Scaria V, Sivasubbu S. Draft Genome Sequence of a Clinical Isolate of Multidrug-Resistant Mycobacterium tuberculosis East African Indian Strain OSDD271. Genome Announc. 2013 Aug 1;1(4). pii: e00541-13. doi: 10.1128/genomeA.00541-13. Bhardwaj A, Bhartiya D, Kumar N, Open Source Drug Discovery Consortium, Scaria V* TBrowse: an Integrative Genomics Map of Mycobacterium tuberculosis. Tuberculosis 2009 Sep;89(5):386-7. doi: 10.1016/j.tube.2009.07.005 | Genome Data Accessions Mycobacterium tuberculosis OSDD493 Accession: PRJNA213484 ID: 213484 Mycobacterium tuberculosis str. OSDD515 Accession: PRJNA213253 ID: 213253 Mycobacterium tuberculosis OSDD105 Accession: PRJNA213252 ID: 213252 Mycobacterium tuberculosis EAI/OSDD271 Accession: PRJNA196573 ID: 196573 Mycobacterium tuberculosis OSDD518 Accession: PRJNA193380 ID: 193380 Mycobacterium tuberculosis OSDD487 Accession: PRJNA193379 ID: 193379 Mycobacterium tuberculosis OSDD326 Accession: PRJNA193378 ID: 193378 Mycobacterium tuberculosis OSDD472 Accession: PRJNA193377 ID: 193377 Mycobacterium tuberculosis OSDD354 Accession: PRJNA193326 ID: 193326 Mycobacterium tuberculosis OSDD500 Accession: PRJNA193323 ID: 193323 Mycobacterium tuberculosis OSDD504 Accession: PRJNA193305 ID: 193305 Mycobacterium tuberculosis OSDD071 Accession: PRJNA193304 ID: 193304 Mycobacterium tuberculosis OSDD630 Accession: PRJNA193298 ID: 193298 Mycobacterium tuberculosis OSDD518 Accession: PRJNA78961 ID: 78961 Mycobacterium tuberculosis OSDD504 Accession: PRJNA78959 ID: 78959 Mycobacterium tuberculosis OSDD071 Accession: PRJNA78807 ID: 78807 |
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