Author: AT Vivek,NIPGR

Arabidopsis thaliana isomiR annotation from sRNA-seq datasets

Here, you'll find essential IsoMiRmap lookup tables for annotating isomiRs of Arabidopsis thaliana, curated and organized for user convenience.

Lookup Tables:

1. ath_LookupTable_isomiRs_miRBase_v22.txt
   This file contains a 'k-mer lookup table' that enables fast mapping while ensuring thorough isomiR mining. Each entry represents a candidate isomiR sequence of k nucleotides, where k ranges from 18 to 26.

2. ath_Mature_Coordinates_miRBasev22_TAIR10.txt
   This file contains the coordinates of mature miRNAs from miRBase.

3. ath_MiRNAspace_HairpinSequences_miRBase_v22_TAIR10.fa
   This file includes a FASTA format of hairpin miRNAs from miRBase.

4. ath_RepeatMakerClassIslands_miRBase_v22.txt
   This file contains repeat islands to determine whether the isomiR can be found within a known repeat element.

5. ath_SNPtable_miRBase_v22.txt
   This file contains sequences that exhibit SNP variations (1001 Genomes Project) compared to the reference isomiR sequence.

These are the tables used to annotate isomiRs available is athisomiRDB.

Feel free to explore and leverage these files for your isomiR analysis in Arabidopsis thaliana.

Citation:

If you find these files useful in your research, please consider citing our work:

If you have any questions or feedback, please don't hesitate to reach out.

Contact: [vivek37373@gmail.com; shailesh@nipgr.ac.in ]

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