User: pltbiotech_tkarthi

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Posts by pltbiotech_tkarthi

<prev • 18 results • page 1 of 2 • next >
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Comment: C: How to use wheat chromosome 3D as input for snpEff?How I can add the wheat refer
... Thanks Lieven Sterck, I added the rephrased question as you have written here. ...
written 13 days ago by pltbiotech_tkarthi70
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Comment: C: How I can add the wheat reference genome database (I need to install 3D chromoso
... Yes, I can retrieve the chromosomal contigs from URGI-IWGSC, but I don't know how to give the chromosomal contig as an input file to snpEff. ...
written 14 days ago by pltbiotech_tkarthi70
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Comment: A: How I can add the wheat reference genome database (I need to install 3D chromoso
... I need to annotate the variants of my gene of interest with VCF file, physically this gene is is located at between 363599046 363598038bp in 3DL chromosome. I already did with VEP ENSEMBL server, but would like to do with snpEff as well to compare the results. ...
written 14 days ago by pltbiotech_tkarthi70
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How to use wheat chromosome 3D as input for snpEff?How I can add the wheat reference genome database (I need to install 3D chromosome based database for the annotation of VCF file from 3D chromosome)?
... How I can add the wheat reference genome database (I need to install 3D chromosome based database for the annotation of VCF file from 3D chromosome. Since I referred the manual of snpEff at: http://snpeff.sourceforge.net/SnpEff_manual.html#run and most of the examples given here based on human g ...
snp written 14 days ago by pltbiotech_tkarthi70
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How to add Triticum aestivum snpEff4.3 genome database or appropriate wheat genome database in Galaxy for VCF annotation?
... I added the T. aestivum snpEff4.3 genome database in Galaxy (https://usegalaxy.org/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpeff%2FsnpEff%2F4.3%2BT.galaxy1&version=4.3%2BT.galaxy1&__identifer=rjgm18erx4), seems the database has been added as I could see theT. aestivum snpEff4.3 gen ...
genome written 19 days ago by pltbiotech_tkarthi70
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Answer: A: cDNA to protein conversion
... You can also use tblastx to search your cDNA query using translated nucleotide database to findout any paralogs or orthologs that match with your wild or mutant sequences. https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=tblastx&PAGE_TYPE=BlastSearch&BLAST_SPEC=&LINK_LOC=blasttab ...
written 20 days ago by pltbiotech_tkarthi70
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Answer: A: Significance of motifs around mutations
... If you have fasta sequence aligned format of your SNP sequences (or you can create aligned SNPs using snp-sites-linux based:https://github.com/sanger-pathogens/snp-sites), then you can import to Tassel or other online softwares to create a Hapmap file. Seperately, use your reference sequence in ENSE ...
written 21 days ago by pltbiotech_tkarthi70
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Answer: A: cDNA to protein conversion
... If you have cDNA or complete transcript, you can just use expasy translate and choose the correct single frame from the 3 frames result from sense strand. ...
written 21 days ago by pltbiotech_tkarthi70
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Answer: A: mean Tajima's D value
... Hello, First of all I don't know which software you have used. If you use, DNAsP, there is a sliding window option to calculate, you could adjust the windows length and size and it will calculate region by region. If not, you don't need to click the sliding window option in DNAsP, the program will ...
written 3 months ago by pltbiotech_tkarthi70
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Answer: A: How to analysis mutations effects bioinformatically?
... I agree with swbarnes2. Bioinformatically you could find out different alleles from a geographic isolates or population even with premature stop codon etc and you could hypothetically translate them to a putative protein, but needs bench wet lab work from biologist to extract proteins (may needs to ...
written 3 months ago by pltbiotech_tkarthi70

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Scholar 3 months ago, created an answer that has been accepted. For A: mean Tajima's D value

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