Tag: Splice

ISOGO – Functional Annotation of Protein-coding Splice Variants

ISOGO

:: DESCRIPTION

ISOGO (ISOform + GO function imputation) is a prediction model of isoform functions based on correlation of isoform expression and protein domains.

::DEVELOPER

ISOGO team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / MacOsX
  • R

:: DOWNLOAD

ISOGO

:: MORE INFORMATION

Citation

Ferrer-Bonsoms JA, Cassol I, Fernández-Acín P, Castilla C, Carazo F, Rubio A.
ISOGO: Functional annotation of protein-coding splice variants.
Sci Rep. 2020 Jan 23;10(1):1069. doi: 10.1038/s41598-020-57974-z. PMID: 31974522; PMCID: PMC6978412.

SpliceDB 1.0 – Splice Graph Proteomics Tools

SpliceDB 1.0

:: DESCRIPTION

SpliceDB is a software of incorporation of RNA-seq for MS database search

::DEVELOPER

CCMS The Center for Computational Mass Spectrometry

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 SpliceDB

:: MORE INFORMATION

Citation

J Proteome Res. 2014 Jan 3;13(1):21-8. doi: 10.1021/pr400294c. Epub 2013 Jul 17.
Proteogenomic database construction driven from large scale RNA-seq data.
Woo S1, Cha SW, Merrihew G, He Y, Castellana N, Guest C, MacCoss M, Bafna V.

Portcullis 1.2.2 – Splice Junction Analysis and Filtering from BAM files

Portcullis 1.2.2

:: DESCRIPTION

Portcullis stands for PORTable CULLing of Invalid Splice junctions from pre-aligned RNA-seq data. It is known that RNAseq mapping tools generate many invalid junction predictions, particularly in deep datasets with high coverage over splice sites.

::DEVELOPER

the Earlham Institute.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Portcullis

:: MORE INFORMATION

Citation

Gigascience. 2018 Dec 1;7(12). doi: 10.1093/gigascience/giy131.
Efficient and accurate detection of splice junctions from RNA-seq with Portcullis.
Mapleson D, Venturini L, Kaithakottil G, Swarbreck D.

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