User: Dattatray Mongad

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340
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Location:
National Centre for Cell Science, Pune
Website:
http://www.nccs.res.in/
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DattatrayMongad
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4 days, 12 hours ago
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3 years, 3 months ago
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Posts by Dattatray Mongad

<prev • 61 results • page 2 of 7 • next >
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Comment: C: Amino Acid matrices freely downloadable url
... See the link [POP][1]. You can also find some references and original scripts to generate the matrix there. [1]: http://www.drive5.com/pop/VTML200I ...
written 13 months ago by Dattatray Mongad340
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Answer: A: Amino Acid matrices freely downloadable url
... BLOSUM and PAM series matrices are available on NCBI ftp. See this link: ftp://ftp.ncbi.nih.gov/blast/matrices/ ...
written 13 months ago by Dattatray Mongad340
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Answer: A: How to plot length distribution of contigs in the assembly?
... use this [Python script][1]. Easy to use: python contigPlot.py fastaDir. Where fastaDir is directory name containing genome files (extension .fasta) [1]: https://github.com/drdee255/code-Util/blob/master/contigPlot.py ...
written 13 months ago by Dattatray Mongad340
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Comment: C: Suggestions for better and accurate tool for PanGenome analysis.
... I have several microbial genomes and protein files from multiple genera. I have tried [BPGA][1] but it cantbe automated. [1]: http://iicb.res.in/bpga/index.html ...
written 15 months ago by Dattatray Mongad340
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Suggestions for better and accurate tool for PanGenome analysis.
... I am doing pan genome analysis of multiple genera. I am searching a tool which will work on protein files (I have annotated proteins for each genome). I wanted to run [Roary][1], but it requires .gff files as well. Any suggestions are welcomed. [1]: https://github.com/sanger-pathogens/Roary/tre ...
genome gene pangenome sequencing written 15 months ago by Dattatray Mongad340
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Answer: A: download genbank sequences with exon sequences highlighted
... You can use efetch from ncbi-entrez-direct utilities. But first, you must have the accessions (with start and end of seuences which you want to extract). Make one file for this data and use following command in any script. efetch -db nuccore -id NG_007524.1 -format fasta -chr_start start -chr_stop ...
written 15 months ago by Dattatray Mongad340
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Answer: A: Programmatically retrieve the length of a gene
... Use [seq_stat.py][1], it will give output as tab-separated file, containg header, count of each nucleotide and sequence length. If multifasta file is provided, it will print this statistics. The sequence length of each sequence will be in last column. [1]: https://github.com/drdee255/Python-code ...
written 15 months ago by Dattatray Mongad340
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Answer: A: Extract Reverse Reads Based on Header Information of Forward Reads
... use [fastq-pair][1], it gives the only reads which are in forward and reverse files. So, rather than making forward.txt(headers), make forward.fastq(containg reads for which you want reverse reads to be extracted) and run the program. This will make four files in the directory: 1. forward.fastq.p ...
written 15 months ago by Dattatray Mongad340
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Answer: A: Continuous mismatch at the end of the alignment, how to eliminate it?
... The trailing unaligned regions are results of global alignments. Use mafft --localpair (local alignment), in which trailing unialign regions from both the ends are not considered in order to maximiza alignment scores. ...
written 16 months ago by Dattatray Mongad340
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Answer: A: Advice for trimming asymmetric adapters for paired end sequencing library
... You can use [trimmomatic][1] for this kind of trimming where you can include your adapters in their adapter library and perform trimming. [1]: http://www.usadellab.org/cms/?page=trimmomatic ...
written 16 months ago by Dattatray Mongad340

Latest awards to Dattatray Mongad

Popular Question 4 months ago, created a question with more than 1,000 views. For Genome annotation to KEGG KO ids
Scholar 4 months ago, created an answer that has been accepted. For A: Amino Acid matrices freely downloadable url
Scholar 9 months ago, created an answer that has been accepted. For A: Amino Acid matrices freely downloadable url
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Amino Acid matrices freely downloadable url
Scholar 13 months ago, created an answer that has been accepted. For A: Amino Acid matrices freely downloadable url
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Amino Acid matrices freely downloadable url
Scholar 16 months ago, created an answer that has been accepted. For A: Extract specific fasta sequences from multiple multi-fasta files located in a di

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