biovino1 / lncrna Goto Github PK
View Code? Open in Web Editor NEWlncRNA folding from sequence
lncRNA folding from sequence
************************************************************************************************************** # DETERMINING LNCRNA STRUCTURE FROM ITS SEQUENCE ************************************************************************************************************** This project takes lncRNA transcripts from a GTF file, locates their positions in the human genome (g37), and obtains their fasta sequence. These sequences are then written out in fasta format to directories depending on their length. This is all performed by the Genome_Reading.py script. Because the end goal of these lncRNA fasta sequences is to see how they fold, sequences are broken up into categories of every 500 base pairs i.e. 1-500, 501-1000, etc. Larger sequences take longer to fold. G37_Parsing.py reads the human genome fasta file and pulls out the sequences of the 23 chromosomes. This was performed so that a local blast database containing only the chromosomes could be used to test the validity of the fasta sequences for each transcript. Resulting fasta files will be uploaded to a university computer cluster. Using Mathews Lab "RNAstructure" package, the secondary structure of these RNA fasta sequences are to be determined. rna_manager.py and rna_manager.slurm were used on the university computer cluster to run RNAstructure package jobs. lnc_fdb.fa and lnc_hc.fa were downloaded from https://lncipedia.org/download. These two fasta files were parsed with lnc_parsing.fa to obtain the individual fasta sequences of each lncRNA transcript. compare_fastas.py was used to compare the fasta sequences gathered from genome_reading.py and lnc_parsing.fa. verify_bases.py was used to read each letter of all fasta sequences in a directory to ensure they were ATCG compliant. Sequences that failed to meet this requirement are written out to bad_bases.txt. ************************************************************************************************************** # WORKFLOW ************************************************************************************************************** Homo_sapiens.GRCh37.dna.alt --> G37_Parsing.py --> g37_chroms.fa lncipedia_5_2_hc_hg19.gtf + Homo_sapiens.GRCh37.dna.alt --> Genome_Reading.py --> Data (folder) lnc_fdb.fa + lnc_hc.fa --> lnc_parsing --> fdbData, hcData (folders) Some manual file manipulation occured: 1) The first line of the gtf file used in this project contained "##gtf" and was deleted before running Genome_Parsing.py. A local blast database was made using g37_chroms.fa on a unix server using the bioinfo module. Several sequences were blasted using this database to ensure they were taken correctly.
A declarative, efficient, and flexible JavaScript library for building user interfaces.
๐ Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. ๐๐๐
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google โค๏ธ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.