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|Alternative name||INDian EXome database|
|Restrictions to use||None|
|Data access||File download, Browse|
|User data submission||Not allowed|
- person_outline Odity Mukherjee
Publication for INDian EXome database
The other white‐nose syndrome transcriptome: Tolerant and susceptible hosts respond differently to the pathogen Pseudogymnoascus destructans
[…] 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) […]
Clustering Molecular Dynamics Trajectories for Optimizing Docking Experiments
[…] ), 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 […]
Whole genome sequencing and methylome analysis of the wild guinea pig
[…] 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 […]
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