CROSSalign

Computes the similarity of RNA secondary structure

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RNA Sequence 1 (FASTA format, please ensure that your sequences only contain A, C, G, T, and U. Do not use !@#$% etc.; the minimum required sequence length is 25 nucleotides.)

This module accepts text in fasta format. There is another version available that allows submission via file upload.

Modes of Dynamic Time Warping (DTW; see the Tutorial/Documentation for the details)

Standard DTW

OBE-DTW

Fragmented OBE-DTW

Dataset (lincRNAs of a specific organism. Ensembl 93, Jul 2018, recent release)

Dataset (lincRNAs of a specific organism. Ensembl 84, Mar 2016, testing set)

Custom Dataset (Upload your sequences for a custom dataset)

Organism (all lincRNAs from Ensembl 93, Jul 2018) recent release

Human

Mouse

Macaque

Rat

Zebrafish

Organism (all lincRNAs from Ensembl 84, Mar 2016) testing set

Human

Mouse

Macaque

Rat

Zebrafish

RNA Sequence 2 (FASTA format, please ensure that your sequences only contain A, C, G, T, and U. Do not use !@#$% etc.; the minimum required sequence length is 25 nucleotides.)

Upload File

RNA Sequences for custom dataset (FASTA format, please ensure that your sequences only contain A, C, G, T, and U. Do not use !@#$% etc.; the minimum required sequence length is 25 nucleotides.)

Just trying out? Use the following examples:

The Rep-A of Orangutan against the Rep-A of Human

D2 of Human against the entire HOTAIR of mouse

HIV genotype AE (2001) vs HIV genotype B (1993)

RepA of Orangutan against all the lincRNAs of human