Neurospora crassa EST Clones to Loci Mapping

Description

There are 10 libraries of expressed sequence tags (ESTs) available for Neurospora. We have associated the clones from these EST libraries to their corresponding gene locus in Neurospora assembly 3.

A single corresponding gene was found for 75% of all the EST clones, and the remaining 25% were left unmapped (70% and 30% respectively for the evening library). A clone is considered as mapped when any of the following is true:

1. Both the forward and reverse reads produce BLAT hits to the same contig, AND
   the forward and reverse reads are on opposite strands, AND
   the annotated gene is located between the forward and reverse reads
2. The clone only has a forward read that produces a BLAT hit, AND
   the annotated gene is within 150 bp downstream of the forward read, AND
   the annotated gene is on the same strand as the forward read
3. The clone only has a reverse read that produces a BLAT hit, AND
   the annotated gene is within 150 bp upstream of the end of the reverse read, AND
   the annotated gene is on the opposite strand as the reverse read

The largest group of unmapped clones (up to 40% of all unmapped) are those whose forward and reverse reads are hitting different genomic contigs. The rest of the cases are currently being examined and classified.

Download

The following files are available for download:

These tab-delimited files represents a single EST library and come in two versions. The first maps EST to loci, with the columns CLONE and LOCUS, in that order. When a clone could not be mapped, NOT_MAPPED is specified as gene locus. The second maps loci to a comma-separated list of ESTs, with the columns LOCUS and CLONES, in that order.

For your convenience, combined files containing all EST clones have also been provided:

The first (EST to loci) has the columns LIBRARY, CLONE and LOCUS, in that order. The second (loci to EST) has the columns LOCUS and CLONES, in that order.