Padlock: Design padlock probes for in-situ sequencing

Input
Results
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Source sequences for target design

Ensembl gene/transcript name(s) or FASTA sequence

Attribute identifier

Feature identifier

FASTA input: Source sequence is absent in reference genome:

Probe design

Probe arm length

Min. genome distance

Use hamming distance (default is edit distance):

Only one arm needs to be unique (default is both arms):

Allow overlapping probes (default is non-overlapping):

Color codes and pre-defined or custom barcodes

Amount of colors

Length of code

Custom barcodes
Color code and barcode file in FASTA format (.fa, .fa.gz). Example:

 >143312
 TCAGGCTAGTGTCCAACGGA
 >112431
 AAATCCGATCGGCCTAACGG

Anchor and spacer sequences

Anchor

Spacer left

Spacer right

Select genome

Application Description

Padlock is a method to design probes for in-situ sequencing.

Accepted Input

You need to input Ensembl gene (e.g., ENSG00000232810) or transcript identifiers (e.g., ENST00000700026). For gene identifiers use "gene_id" as attribute and "transcript_id" for transcript identifiers. Gene symbols are currently not supported. Alternatively, you can also input a FASTA sequence with a header like ">Input" followed by the actual sequence. For FASTA input, you need to specify whether the sequence is present in the genome (default) or absent.

Sample Data

The "Show Example" button loads an example reference genome with matching Ensembl gene identifiers.