Bioinformatics Softwares
Bioinformatics softwares developed at NABI:
Lathyrus Sequence Search
Lathyrus Sequence Search Link: https://lathyrusgenome.nabi.res.in/blast/
Description: The sequence search option offers a BLAST search of the Lathyrus CDS, mRNA, protein and whole genome sequences via Sequence Server implementation. Input can either be protein or DNA sequences in FASTA format.
Blast Database Files :
1) “Lathyrus final CDS”: Coding sequences of Lathyrus sativus.
2) “Lathyrus final mRNA”: mRNA of Lathyrus sativus.
3) “Lathyrus genome”: Whole genome assembly of Lathyrus sativus.
4) “Lathyrus final proteins”: Protein sequences of Lathyrus sativus.
Citation: S. Rajarammohan, L. Kaur, A. Verma, D. Singh, S. Mantri, J. K. Roy, T. R. Sharma, A. Pareek & P. K. Kandoth, "Genome sequencing and assembly of Lathyrus sativus - a nutrient-rich hardy legume crop", Scientific Data, Volume 10, Issue 1, Pages 32
Disclaimer: The purpose of this sequence search facility is only for non-profit educational use.
North East Indian Rice Project:
The North-Eastern region (NER) of India is known for its rich diversity of indigenous rice landraces. This region is a hotspot for rice biodiversity. Black rice and Joha rice are two distinct varieties of rice from the NER of India, and they are known for their unique characteristics such as anthocyanin content, which is a type of antioxidant. Black rice, also known as Chakhao in Manipur, is famous for its dark purple-black grains. This color is due to its high anthocyanin content. Unlike black rice, Joha rice has a low anthocyanin content and is primarily valued for its aromatic qualities and taste. The accumulation of significant levels of anthocyanin is a characteristic associated with the process of rice domestication. Thus, gaining insights into the genetic underpinnings of this trait is not only essential for enhancing rice quality but also yields valuable insights into the domestication history of rice. This project employed a pan-genome approach along with data from RNA-seq and small RNA-seq analyses conducted at various developmental stages of the grain which is a valuable resource to investigate the origins, domestication history, and anthocyanin biosynthesis pathways of Black rice. With this project, not only the genome assembly of North-Eastern region of India rice landraces has been made available in the public domain but also the comparative pan-genomic analysis of 8 NER genomes.
Sequence Search Link: Please click
Description: The sequence search option offers a BLAST search of the North-Eastern region (NER) of India rice landraces via Sequence Server implementation. Input can either be protein or DNA sequences in FASTA format.
Blast Database Files: Eight rice genotypes
KolaJoha: de novo genome assembly of aromatic rice from the North Eastern region of India, i.e., Kola Joha
NER1: Chakhao Amubi
NER2: Chakhao Poireition
NER3: Black rice
NER4: Manipur Black rice
NER5: Maniki Madhuri Joha
NER6: Keteki Joha
NER7: Kola Joha
NER8:KonJoha
Citation: P.K Singh, H. C. Rawal, A.K. Panda , J. Roy , T.K. Mondal & T. R. Sharma, “ Pan-genomic, transcriptomic, and miRNA analyses to decipher genetic diversity and anthocyanin pathway genes among the traditional rice landraces”, Genomics, Volume 114, Issue 5, Pages 110436
Disclaimer: The purpose of this sequence search facility is only for non-profit educational use.
Software Name: SSFinder
Publication Title: SSFinder: High Throughput CRISPR-Cas Target Sites Prediction Tool
Publication Abstract: Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein (Cas) system facilitates targeted genome editing in organisms. Despite high demand of this system, finding a reliable tool for the determination of specific target sites in large genomic data remained challenging. Here, we report SSFinder, a python script to perform high throughput detection of specific target sites in large nucleotide datasets.The SSFinder is a user-friendly tool, compatible with Windows, Mac OS, and Linux operating systems, and freely available online.
Publication Download Link: Download (PDF File, 1.32mb)
Software Download Link: Download (Zip file, 2kb)