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Table of Contents

 

Searching protein domains on alternatively spliced regions of human gene TNNT1

According to RefSeq (NM_003283), 

This gene encodes a protein that is a subunit of troponin, which is a regulatory complex located on the thin filament of the sarcomere. This complex regulates striated muscle contraction in response to fluctuations in intracellular calcium concentration.


Input

  • Annotation of eight alternative transcripts from GENCODE Basic v24 (Download)
  • Chromosome 19 FASTA file from GRCh38/hg38 (Download)
  • Reference file (Download)
  • HMM file (Download)

Command-lines

 

Code Block
titleObtaining reference transcript sequence
$> astalavista -t astafunk --tref --gtf tnnt1.gtf --genome ~/example/genome/ > reference_tx.fasta
Code Block
titleCreating reference file
$> hmmsearch --domtblout reference_file ~/Databases/Pfam/Pfam-A.hmm reference_tx.fasta
Tip
titleObtaing a reduced HMM file
Code Block
$> grep -v "#" reference_file | awk '{print $5}' | sort | uniq | hmmfetch -f ~/Pfam/Pfam-A.hmm - > database.hmm

 

or skip these commands and use directly the whole database Pfam-A.hmm as parameter for the option [–hmm].

Code Block
titleRunning AstaFunk to obtain alternatively spliced domains
astalavista -t astafunk --all --genome ~/example/genome/ --gtf tnnt1.gtf --reference reference_file --hmm database.hmm

Description of the output columns can be found in 3.4 - Tool ASTAFUNK (Prediction of functional domains impacted by AS).