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Introduction

StartScan recognizes translation initiation sites in human DNA sequences (Article).

Usage

Sequences should be submitted in the FASTA-format. Each sequence in the FASTA format begins with a single-line description, followed by lines of DNA sequence data. The description line must begin with a greater-than (">") symbol in the first column. An example is give below.

>AB000263 |acc=AB000263|descr=Homo sapiens mRNA 
ACAAGATGCCATTGTCCCCCGGCCTCCTGCTGCTGCTGCTCTCCGGGGCCACGGCCACCGCTGCCCTGCC
CCTGGAGGGTGGCCCCACCGGCCGAGACAGCGAGCATATGCAGGAAGCGGCAGGAATAAGGAAAAGCAGC
CTCCTGACTTTCCTCGCTTGGTGGTTTGAGTGGACCTCCCAGGCCAGTGCCGGGCCCCTCATAGGAGAGG
AAGCTCGGGAGGTGGCCAGGCGGCAGGAAGGCGCACCCCCCCAGCAATCCGCGCGCCGGGACAGAATGCC
CTGCAGGAACTTCTTCTGGAAGACCTTCTCCTCCTGCAAATAAAACCTCACCCATGAATGCTCACGCAAG
TTTAATTACAGACCTGAA

A file called startscan_annotation is generated that contains the translation initiation site recognitions. Each recognition is on one line:

position	{start,start_rev}	score

with position indicating the sequence position where the site is located (i.e. the position of the A of the ATG and the C of the CAT (ATG reverse complement)). Next to the position is the type of the site (start_rev indicating a TIS on the reverse strand). Next to the type is the score given by the site classification model.

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