avrilcoghlan

#!/usr/local/bin/perl

# 
# Perl script treefam_QC5.pl
# Written by Avril Coghlan ([email protected])
# 4-Feb-09.
# Updated 26-June-09 to work with TreeFam release 8.
#
# This perl script finds cases where a full gene set for a species was
# loaded into the TreeFam mysql database, but no genes from that species

avrilcoghlan

#!/usr/local/bin/perl

# 
# Perl script treefam_QC6.pl
# Written by Avril Coghlan ([email protected])
# 4-Feb-09.
#
# This perl script finds cases where more than one alternative splice form
# from the same gene was added to a family.
#

avrilcoghlan

#!/usr/local/bin/perl

# 
# Perl script treefam_QC7.pl
# Written by Avril Coghlan ([email protected])
# 4-Feb-09.
#
# This perl script finds cases where more different alternative splices of
# the same gene do not have unique transcript ids in the 'genes' table.
#

avrilcoghlan

#!/usr/local/bin/perl

# 
# Perl script treefam_QC8.pl
# Written by Avril Coghlan ([email protected])
# 4-Feb-09.
#
# This perl script finds cases where a transript listed in the 'genes' table
# is missing an amino acid sequence in the 'aa_seq' table or missing a
# DNA sequence in the 'nt_seq' table.

avrilcoghlan

#!/usr/local/bin/perl

# 
# Perl script treefam_QC9.pl
# Written by Avril Coghlan ([email protected])
# 3-Feb-09.
#
# This perl script finds TreeFam transcripts that appear in the fam_genes
# table, but do not appear in the 'genes' table.
#

avrilcoghlan

#!/usr/local/bin/perl

# 
# Perl script treefam_QC10.pl
# Written by Avril Coghlan ([email protected])
# 4-Feb-09.
#
# This perl script finds TreeFam proteins were added to a particular
# family, but actually have a stronger hmmer match to a different family.
#

avrilcoghlan

#!/usr/local/bin/perl

# 
# Perl script treefam_QC11.pl
# Written by Avril Coghlan ([email protected])
# 5-Feb-09.
#
# This perl script finds cases where different alternative splices of the
# same gene were put into different families, but those alternative splice
# forms overlap a lot at the DNA level.

avrilcoghlan

#!/usr/local/bin/perl

# 
# Perl script treefam_QC12.pl
# Written by Avril Coghlan ([email protected])
# 6-Feb-09.
#
# This perl script checks for cases where a TreeFam family seems to have
# disappeared from a particular version of TreeFam, even though it was
# present in the previous version of TreeFam and has not been curated since.

avrilcoghlan

#!/usr/local/bin/perl

# 
# Perl script treefam_release2.pl
# Written by Avril Coghlan ([email protected])
# 10-Feb-09.
#
# This perl script prints out the total number of genes in families,
# and the total number of families, in a particular TreeFam release.
#

avrilcoghlan

#! /usr/bin/perl

# 
# Perl script count_worm_paralogs2b.pl
# Written by Avril Coghlan ([email protected])
# 1-Oct-08.  
#
# This perl script reads in the trees in TreeFam-6 that a pair of
# worm paralogs are in, and calculates information about the paralogs 
# and the tree.