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INDEX-db specifications

Information


Unique identifier OMICS_29347
Name INDEX-db
Alternative name INDian EXome database
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Version 1.14.1
Maintained Yes

Maintainer


  • person_outline Odity Mukherjee

Additional information


http://jbrowse.org/jbrowse-1-14-1-maintenance-release/

Publication for INDian EXome database

INDEX-db citations

 (3)
library_books

The other white‐nose syndrome transcriptome: Tolerant and susceptible hosts respond differently to the pathogen Pseudogymnoascus destructans

2017
Ecol Evol
PMCID: 5606880
PMID: 28944007
DOI: 10.1002/ece3.3234

[…] resulting trimmed paired‐end reads were combined prior to alignment. We originally planned to align reads to the available M. lucifugus genome (Myoluc2.0; http://www.ensembl.org/Myotis_lucifugus/Info/Index?db=core; Cunningham et al., ), but alignment of reads was low (~28%). We therefore used Trinity v2.2.0 (Grabherr et al., ) to generate a de novo transcript assembly in strand‐specific mode (RF) […]

library_books

Clustering Molecular Dynamics Trajectories for Optimizing Docking Experiments

2015
Comput Intell Neurosci
PMCID: 4385651
PMID: 25873944
DOI: 10.1155/2015/916240

[…] ), since they already have the coenzyme as part of their structures.The experiments were divided into two steps. In the first step, we identify the best k value for k-means clustering based on Dunn's index, DB, and the gap statistic. In the second step, we perform exhaustive docking experiments on the FFR model and 20 different compounds to validate the best clustering solution. Additionally, we a […]

library_books

Whole genome sequencing and methylome analysis of the wild guinea pig

2014
BMC Genomics
PMCID: 4302102
PMID: 25429894
DOI: 10.1186/1471-2164-15-1036

[…] Ssaha2 (v.2.5.5; []) was used to map the MP and mDNA-enriched reads (not yet bisulfite-treated) onto the C. porcellus reference sequence cavPor3 (http://www.ensembl.org/Cavia_porcellus/Info/Index?db=core). In order to preserve as many differences as possible between C. aperea and C. porcellus, we allowed a high error rate of 20% per read. The maximum gap size allowed for each library was […]

Citations

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INDEX-db institution(s)
National Centre for Biological Sciences, Bengaluru, India; Institute of Bioinformatics and Applied Biotechnology, Bengaluru, India; Institute for Stem Cell Biology and Regenerative Medicine, Bengaluru, India; National Institute of Mental Health and Neuro Sciences, Bengaluru, India
INDEX-db funding source(s)
Supported by government funded research grant under the aegis of Department of Biotechnology (grant number BT/PR17316/MED/31/326/2015), Pratiksha trust, and the Department of Biotechnology (grant number BT/PR12422/MED/31/287/2014).

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