sRNAcons

Conservation depth estimation of small RNAs

Description

User provided small RNA sequences (fasta format) are mapped against all assemblies available in sRNAtoolbox. The tool has two different outputs, i) The conservation depth for all small RNA input sequences, i.e the percentage of genomes in which the sequence was found, and ii)the percentage of mapped input sequences per genome.

Input

The input should be a fasta file containing the small RNA sequences for which you want to estimate the conservation depth (e.g. a set of mature miRNAs). This file can be uploaded to the server or provided via URL. You can also choose the number of mismatches you want to allow in the sequence alignment and the kingdom (animal or plants) against which you want to align your sequences.

Results

1. Graphic summary: a. Top 20 conserved miRNAs

   

   b. Top 20 species with the highest number of conserved sRNAs

   

2. Conservation depth per sRNA: The user can visualize/download a table with the conservation depth per sRNA sequence, including the frequency and a list of species in which the sequence is conserved per sRNA.

3. Conservation depth per species: The user can visualize/download a table with the frequency of the input sRNAs per species.