Rahul Arvind Jamdade

11 Questions 48 Answers 0 Followers

Questions related from Rahul Arvind Jamdade

How to simulate/generate DNA sequences with reference to the Singletone Species?

I am having many singleton Species (species representing only one DNA sequence). These singletons lack resolution potential as they are single, when applied machine learning classifiers singletons...

09 September 2019 3,083 3 View

How to generate Synthetic DNA barcode dataset?

Help appreciated!! We are having Empirical data sets of plant barcodes (matK, ITS and rbcL), and want to compare analytical methodology used for Empirical data sets with the Synthetic data...

09 September 2019 952 8 View

Which are most preferred Alignment-free tools for matK and ITS2?

I have NCBI GenBank mined DNA sequences belonging to matK and ITS2 regions. I would appreciate if anyone suggests alignment free tools to calculate K-mer frequencies OR Genetic distances in order...

09 September 2019 2,736 5 View

How to remove ambiguous DNA characters form mulit-sequence FASTA file?

I am having unaligned multiple sequence FASTA file (don't want to align) with ambiguous characters: RYWSMKHBVDNS I want to remove/delete those characters... 1) I tried with mEMBOSS Readme:...

12 December 2017 3,227 7 View

Alignment-free methods: Dealing with compression-based methods for DNA barcode analysis?

Used Software: GenCompress (Download link: http://www.cs.cityu.edu.hk/~cssamk/gencomp/downGen.htm) Description: I have used test file (FASTA format: Mined from NCBI GenBank), as an input, named...

12 December 2017 393 2 View

Dealing with Mined DNA sequence: HELP in Alignment & Analysis?

I am dealing with some mined DNA sequences from GenBank of flowering plants (rbcL and matK gene), to construct phylogenetic tree out of them for finding better taxonomic resolution. ...

10 October 2017 3,307 6 View

How do you find the K-mer size of a nucleotide sequence?

The size of K-mers is between 1 and 8, for nucleotide sequence it is recommended from 4 to 7. The programs found were all in Python, Pearl, Linux or C language which are not userfriendly. Please...

03 March 2015 1,860 9 View

Can anyone suggest software, R code or perl code for determining monophyla, where input is given in tree format (Newick file)?

I am having thousands of samples (DNA barcoded) for species confirmation (False positive or True positive species). This species confirmation is to be done on distance based and tree based...

08 August 2014 9,028 7 View

Can anyone assist with a query regarding R package, SPIDER (SPecies IDentity and Evolution)?

I am using R package, "SPIDER" (SPecies IDentity and Evolution), I got its tutorial, which describes analysis for: anoteropsis, dolomedes and sarkar files (input file .rda). The tutorial works...

08 August 2014 3,470 6 View

DNA barcoding, querry regarding tree based (cluster) methods for species identification?

I am working on success rate of DNA barcoding in identification of species using distance and tree based methods. Regarding distance based method, I have used Adhoc and species identifier and...

07 July 2014 6,166 11 View

Where can we get best webcourse on Python for Biologist or Bioinformatics?

Where can we get best web-course beginning from basic Python programming and using Kernels till analyzing data with Machine learning algorithms. I think most of the Biologist don't need much to...

01 January 1970 9,549 5 View