Algorithm



Sl. No. Name of Algorithm Url/Detail
1. WebSynCod:Web Based Software for Synonymous Codon Usage Indices WenSYNCod provides online facility for gene expression identification using synonymous codon usage analysis after it is hosted through a web server. It can save time by doing complex calculations automatically on its own and generating results in understandable format. The software is user friendly and does not demand expertise of computer programming.
2. GSAQ: An innovative statistical approach for identification of potential genes https://cran.r-project.org/web/packages/ GSAQ
3. ProtSComp: Web tool for protein structure comparison using elastic shape analysis approach. An efficient algorithm has been developed for comparing protein structures using elastic shape analysis in which the sequence of 3D coordinates atoms of protein structures supplemented by additional auxiliary information from side-chain properties are incorporated. The performance of the developed algorithm is tested and found to be more efficient. Also, user friendly web-based application called ProtSComp has been developed using above algorithm for comparing protein 3D structures and is accessible free.
4. Statistical Methodology: Simultaneous selection of genotypes for both high yield and stability. A new concept involving an index to select cultivars simultaneously for high yield and stability has been developed and tested on multi-location trial data of rice crop from All India Coordinated Rice Improvement Programme.
5. Statistical Methodology: Development of core set of rice/blackgram germplasm using mixture data. An approach has been developed to identify a core set of germplasm based on the response from a mixture of qualitative (single nucleotide polymorphism genotyping) and quantitative data.
6. Statistical Methodology: Splice site and gene structure prediction An approach for finding association among nucleotide bases in the splice site motifs is developed and used further to determine the appropriate window size for effective identification of features at donor splice sites. Besides, an approach for prediction of donor splice sites using sum of absolute error criterion has also been developed.
7. Statistical Methodology: Prediction of breeding values from genome wide Single Nucleotide Polymorphisms (SNPs) Genomic prediction is meant for estimating the breeding value using molecular marker data which has turned out to be a powerful tool for efficient utilization of germplasm resources and rapid improvement of cultivars. Model-based techniques have been widely used for prediction of breeding values of genotypes from genomewide association studies. However, application of the random forest (RF), a model-free ensemble learning method, is not widely used for prediction. Hence, RF regression model has been applied to predict the kernel length in maize using the genomewide SNPs. The optimum values of tuning parameters of RF have been identified and applied to predict the breeding value of genotypes based on genomewide single-nucleotide polymorphisms (SNP), where the number of SNPs (P variables) is much higher than the number of genotypes (n observations) (P >> n). The prediction accuracy of RF regression was found to be higher that the model based prediction accuracy of breeding values.
8. Statistical Package: corrDNA ā€“ A package in R software https://cran.r-project.org/web/packages/corrDNA/index.html
9. SAS code & C-program A user-friendly computer programme in ā€˜Cā€™ language was developed to select genotypes simultaneously for yield and stability when cultivars are raised over different locations and over years.
10. Databank of resource augmented and Knowledge Generated under Basic and strategic research in frontier areas of Agricultural Sciences http://bioinformatics.iasri.res.in/NAIP4BSR/naipc4/

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