BLAT

Perform a BLAT search using the UCSC Genome Browser.

Arguments

Name	Short	Long	Description
Sequence Type	`-s`	`--seqtype`	Specify the structure format [default: dna] [possible values: dna, protein, translated-rna, translated-dna]
Database Name	`-d`	`--db-name`	Specifies the database name to query [default: hg38]
Output	`-o`	`--output`	optional filepath to write output to [default=stdout]

Command Line Interface

# query UCSC genome browser for the first 121 bp of AP2S1
ggetrs ucsc blat GGGCCCTACAACTGCACCCTGAGCCGGAGCTGCCCAGTCGCCGCGGGACCGGGGCCGCTGGGGTCTGGACGGGGGTCGCCATGGTAACGGGGGAGCGCTACGCCGGGGACTGGCGGAGGG

Python

import ggetrs

# query UCSC genome browser for the first 121 bp of AP2S1
ggetrs.ucsc.blat(
  "GGGCCCTACAACTGCACCCTGAGCCGGAGCTGCCCAGTCGCCGCGGGACCGGGGCCGCTGGGGTCTGGACGGGGGTCGCCATGGTAACGGGGGAGCGCTACGCCGGGGACTGGCGGAGGG"
)

# query UCSC genome browser with amino acid sequence
ggetrs.ucsc.blat(
  "MIRFILIQNRAGKTRLAKWYMQFDDDEKQKLIEEVHAVVTVRDAKHTNFVEFRNFKIIYRRYAGLYFCICVDVNDNNLAYLEAIHNFVEVLNEYFHNVCELDLVFNFYKVYTVVDEMFLAGEIRETSQTKVLKQLLMLQSLE",
  seqtype="protein"
)