Location of motif · Biostar

This is a test version of Biostars. For the public version, visit https://www.biostars.org.

Location of motif

Hi all,

I have found some simple sequence repeat (SSR) using BatchPrimer3 tools on some gene sequence of Rice. Now I want to find the location of these SSRs, where the repeat located on the coding or non-coding (UTR) region of gene sequences, I can do it using Rice genome browser for one gene at the time, but it's time-consuming for many genes. Could you please let me know how I can perform it for many genes?

Thanks in advance

blast genome

• 1,435 views • link

updated 3.1 years ago by Ram

• written 8.8 years ago by coolmsandhu •

Please provide some example data.

• 0 views • link

written 8.8 years ago by shenwei356

0 answers

No answers yet.

Log in to answer this question.

More posts like this

How to extract CDS from WGS data in rice?
written 1.4 years ago by ChanderKant (CK) Chaudhary •

Dear All, I would like to confirm that I am extracting the CDS from WGS data correctly. Below are the steps I followed: 1. Generated …
Understanding Variant Effect Predictor results
written 5.5 years ago by caro-ca •

I am studying the effect of transposable elements in Saccharomyces cerevisiae populations. The outcome I have from Variant Effect Predictor is as follow: Category Count …
SSR marker discovery from RNA-seq data when a reference genome is available
written 9.4 years ago by seta

Hi all, I have Illumina reads (36bp, single end) from mRNA sequencing of human samples in two different conditions. I want to find the probable …
How to extract whole gene sequence with 5' and 3' UTR from genome
written 9.6 years ago by Bioinfonext

I found that in Radish some of the CDS (coding) gene sequences is very similar to each others so I want to extract whole gene …
Selecting primary transcript for each locus from a GFF file
written 10.9 years ago by arnstrm

Hello, I am planning to use Maker predicted genes for identifying orthologs among the closely related species. But Maker has predicted multiple transcripts for each …
Finding coding and UTR regions for a gene list
written 10.9 years ago by seta

<p>Hi all,</p> <p>I have a gene list from human and want to find the location of some simple sequence repeats, which the repeat located on …
Finding coding and UTR regions for a gene list
written 10.9 years ago by seta

<p>Hi all,</p> <p>I have already found some simple sequence repeat (SSR) using MISA, SSRlocator tools on some gene sequence of human. Now I want to …
Finding simple sequence repeat (SSR) on differentially expressed RNA-seq reads
written 11.7 years ago by seta

Hi everybody, I found differentially expressed genes and miRNA derived from Illumina mRNA-seq and miRNA-seq experiments, respectively. Now, I would like to find simple sequence …
Different Repeat Motif
written 14.8 years ago by Nur •

<p>Hi, </p> <p>I've sequence pcr products of some rice varieties (PCR using the same SSR primer), but it turned out that the repeat motif carried …
Finding Minisatellite Repeat Motives In Dna
written 16.0 years ago by Eric Normandeau

<p>Hi,</p> <p>I have contigs representing genes of interest that have been 454 sequenced from BAC libraries. The BAC inserts are about 100kb long and end …