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IARI - RKMP Associated Partners
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Bioinformatics Tools Used in Plant Genomics & Molecular Breeding
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Applications |
Softwares |
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Vector trimming, quality
checking & assembly of high-throughput
genome sequences
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Phred, Phrap & Consed
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Sequence Annotation &
Assembly
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BioEdit, MEGA , DNASTAR &
Softberry: FGNESH
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Multiple nucleotide & protein
sequence alignment
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CLUSTALW, BioEdit , DNASTAR &
MEGA
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Nucleotide & protein sequence
homology searches
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BLASTN, Mega-BLAST, BLASTX,
BLASTP:
On-Line BLAST (NCBI, EMBL & DDBJ) & Local
BLAST (DNASTAR & BioEdit)
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In silico
microsatellite repeat-motifs
mining & Primer designing
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SSRIT - GRAMENE, BatchPrimer3
- USDA & MISA- Gatersen Lab
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PCR primer designing:
Standard PCR, multiplex PCR, Allele specific SNP primers, Q-PCR & Probe
designing
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Primer3, Fast PCR, IDT Q-PCR
assay & BatchPrimer3
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Marker based genetic
diversity analysis & determination of phylogenetic relationships
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NTSYSpc, TREECON,
PowerMarker, PAUP & PAML
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Sequence based molecular
diversity analysis & phylogenetics
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MEGA, DNASTAR, BioEdit &
CLUSTALW
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Bootstrap analysis to
determine confidence limits of dendrogram
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WinBoot, MEGA, DNASTAR,
TREECON & TreeView
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Nucleotide diversity,
synonymous & non-synonymous substitutions (SNPs), genetic distance & phylogeny
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MEGA, DNaSP & PAML
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Population genetic structure
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STRUCTURE
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Mutation models (like
Step-wise) of microsatellites
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Bottleneck & Darwin
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Allele frequency, PIC,
Haplotype frequency, LD based association mapping & phylogenetic analysis
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PowerMarker, MEGA, DNaSp &
GGT
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Kinship coefficient &
population allele frequency
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SPAGeDi, STRUCTURE,
PowerMarker & GGT
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LD based association mapping
of genes/QTLs for complex traits
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TASSEL, PowerMarker & GGT
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Construction of genome maps
(Gene/QTL mapping)
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MAPMAKER, MapQTL, WinQTL,
PowerMarker & GGT
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Graphically representing the
genetic & physical linkage map on chromosomes
using the markers & QTLs
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MapChart & Graphical
GenoTypes (GGT)
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Detection of sequence
variants/mutations (SNPs & InDels) for TILLING
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Autosnip, PolyPhred, MEGA &
CODDLE
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Conversion of SNPs to
cost-effective CAPS markers
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SNP2CAPS, NEB Cutter,
BioEdit, DNASTAR & dCAPS Finder
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Normalization, clustering,
PCA, Differential expression, & gene ontology & pathway analysis of Affymetrix
GeneChip Microarray data
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GeneSpring GX
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Disclamer
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RKMP Team
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