probe_designer

Brief introduction

This program is intended to design padlock probe for spatial transcriptome. When input with gene list you are interested in, the program will search for the corresponding mRNA sequence for the gene and, with some strategy, search for binding sites of specific length you assign.

Binding site search strategy

Current strategy for binding site search is bruteforce. The program will begin in the middle of a mRNA sequence and extend with a step length(length of mRNA sequence divided by binding site length) to both side. You will get n binding site sequences, where n is the maxium of your intended number and the max number you can get from a mRNA sequence.

After that, the binding site sequences will be selected by blast(specificity), G content and consecutive G, which will make a lot of misses in the seq process because we use bicolor coding and G is double off.

The process and tmp file in the process

Get gene_id from ncbi dataset

By the gene name list given, from

Get genbank file of each mRNA from ncbi dataset

Binding site searcher

Blast and decoding of blast_results

tip: blast length is limited to about 1200 sequences once, so split the gene name list if target gene number is too large.

Select wanted binding site by specific rules

Present rules:

1. sequence type is mRNA (judge by genbank file);
2. binding site sequence is specific to this gene in interested organisms (judge by blast results);
3. G percentage is between 40% and 70%;
4. G is not consecutive up to 5 or more;
5. binding site sequence is plus/minus to target gene;

Export not-found gene file for next round search

Considering the error occurred in the id or sequencing searching, sift out in selection, the files of each step are saved as tmp file in "results/time" folder.

Merge the results got from above

run merge.ipynb to merge results got above and return a xlsx file of wanted binding sites for each gene.

Perspective and plans