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CROSSalign

CROSSalign

CROSSalign predicts the structural similarities of two RNA profiles of different length. The tool is based on CROSS and a Dynamic Time Warping algorithm.



 

Submission reference: 215100


Submission label (optional)



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.)



Email address (optional, used for notification)



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.)




Submission status:



Sample data

Just trying it out? Pre-populate the form with: (Please, check that you do not have active proxies!)

Xist Rep-A (Standard DTW) - The Rep-A of Orangutan against the Rep-A of Human
HOTAIR D2 (DTW-OBE) - D2 of Human against the entire HOTAIR of mouse
HIV RNA (fragmented OBE-DTW) - HIV genotype AE (2001) vs HIV genotype B (1993)
Orangutan RepA VS human lincRNAs - RepA of Orangutan against all the lincRNAs of human