LINDEL – Integrated Design system for LincRNA deletion

LINDEL

:: DESCRIPTION

LINDEL is the Integrated Design system for LincRNA deletion (LINDEL) , which was implemented on an interactive web genome-browser. LINDEL system makes possible the design of sgRNAs that i) are based on improved annotations of human and mouse lincRNA genes, ii) function as pairs for the deletion of both whole and segmental regions of these genes, again based on comprehensive functional annotations, and iii) efficiently generate mutations because of both sequence- and secondary structure-based features.

:: DEVELOPER

BIG Lab. (BIOINFORMATICS & GENOMICS)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation:

Lee HJ, Gopalappa R, Sunwoo H, Choi SW, Ramakrishna S, Lee JT, Kim HH, Nam JW.
En bloc and segmental deletions of human XIST reveal X chromosome inactivation-involving RNA elements.
Nucleic Acids Res. 2019 May 7;47(8):3875-3887. doi: 10.1093/nar/gkz109. PMID: 30783652; PMCID: PMC6486550.

Sebnif 1.3rc – Comprehensive Novel lincRNA Filter from RNA-seq data

Sebnif 1.3rc

:: DESCRIPTION

Sebnif (self-estimation based novel lincRNA filter pipeline) is an integrated bioinformatics pipeline for the identification of novel large intergenic noncoding RNAs (lincRNAs)–application in human skeletal muscle cells.

::DEVELOPER

Dr. Sun Hao’s Bioinformatics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
R package
Perl

:: DOWNLOAD

Sebnif

:: MORE INFORMATION

Citation

PLoS One. 2014 Jan 6;9(1):e84500. doi: 10.1371/journal.pone.0084500. eCollection 2014.
Sebnif: an integrated bioinformatics pipeline for the identification of novel large intergenic noncoding RNAs (lincRNAs)–application in human skeletal muscle cells.
Sun K1, Zhao Y2, Wang H2, Sun H1.

iSeeRNA 1.2.2 – Accurate and Extra-fast lincRNA/mRNA Classifier

iSeeRNA 1.2.2

:: DESCRIPTION

iSeeRNA is a support vector machine (SVM)-based classifier for the identification of lincRNAs.

::DEVELOPER

Dr. Sun Hao’s Bioinformatics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX/ Windows
Perl

:: DOWNLOAD

iSeeRNA

:: MORE INFORMATION

Citation

BMC Genomics. 2013;14 Suppl 2:S7. doi: 10.1186/1471-2164-14-S2-S7. Epub 2013 Feb 15.
iSeeRNA: identification of long intergenic non-coding RNA transcripts from transcriptome sequencing data.
Sun K1, Chen X, Jiang P, Song X, Wang H, Sun H.