<commit_before>###############################################################################
#   
#   Name:           Monodelphis_domestica.ini
#   
#   Description:    Configuration file for Opossum Ensembl
#
###############################################################################

#################
# GENERAL CONFIG
#################
[general]

# Database info: only specify values if different from those in DEFAULTS

ENSEMBL_PREDICTION_TEXT_CORE    = Gene structures annotated by a preliminary run of the Ensembl annotation pipeline, only using GeneWise models generated from alignments of proteins from Uniprot. The models have been filtered to form non-redundant sets of transcripts for each gene.
ENSEMBL_SEARCH_IDXS = [ Domain Gene GenomicAlignment Marker Sequence ]

# Assembly info
ENSEMBL_PREFIX       = ENSMDO

ASSEMBLY_ID          = MonDom 2.0
ENSEMBL_GOLDEN_PATH  = BROADO2
ASSEMBLY_DATE        = 2005-05

GENEBUILD_BY         = Ensembl
GENEBUILD_DATE       = 2005-10
SPECIES_RELEASE_VERSION = 2

ENSEMBL_CHROMOSOMES  = []

# Search config
ENSEMBL_SEARCH_IDXS = [  Domain Family Gene GenomicAlignment Marker Sequence ]

# Das
#ENSEMBL_DAS_MAPMASTER_DSN = ;DAS mapmaster for "uploadable DAS"

ENSEMBL_BUM = Scaffold

# Display info
SPECIES_COMMON_NAME  = Opossum
SPECIES_BIO_NAME     = Monodelphis domestica
SPECIES_DESCRIPTION  = opossum
SPECIES_CODE         = md
SPECIES_GROUP        = Mammals
GENERATE_HOME_PAGE   = yes
CYTOVIEW_ENABLED     = 1

##################
# DATABASE CONFIG
# Change the values to the local names of these databases
##################

[databases]
ENSEMBL_DB      = %_core_%

# You can overide the default settings (in DEFAULTS.ini) for specific
# databases. To do this, create an ini-file for this species e.g.
# public-plugins/mirror/conf/ini-file/Monodelphis_domestica.ini with
# the section you wish to overwrite (see the example INI file:
# public-plugins/mirror/conf/ini-files/Genus_species.ini

####################
# Help Database Config
####################

[ENSEMBL_HELP] 
# Accept defaults


####################
# Species-specific colours
####################

[ENSEMBL_STYLE]

[ENSEMBL_COLOURS] 
# Accept defaults


####################
# External Database ad Indexer Config
####################

[ENSEMBL_EXTERNAL_DATABASES]
# Accept defaults

[ENSEMBL_EXTERNAL_INDEXERS]
# Accept defaults


#############
# DAS CONFIG
#############

[ENSEMBL_INTERNAL_DAS_SOURCES]

[PDB_Spice]

[Phenotypes]

# None


####################
# Configure External Genome Browsers
####################

[EXTERNAL_GENOME_BROWSERS] 
# None

####################
# Configure External URLs
# These are mainly for (1) External Genome Browse  {EGB_ }
#                      (2) DAS tracks              {DAS_ }
####################

[ENSEMBL_EXTERNAL_URLS]

####################
# Configure blast data sources. 
# Used in blastview to generate database dropdown
####################
[ENSEMBL_BLAST_METHODS]
# Registers blast methods. Key values are the
# Bio::Tools::Run::Search classes used to run the search 
# Accept defaults

[BLAST_DATASOURCES]
# Registers blast datasources. Key values are used as labels.
# Keys should be registered against methods in species.ini files
# Accept defaults

[BLASTN_DATASOURCES]
# Sequence databases to use with search method (BLASTN)  
# Filesystem location set by DEFAULTS:ENSEMBL_BLAST_DATA_PATH
# Data available from ftp://ftp.ensembl.org/pub/current_mouse/data/fasta/
DATASOURCE_TYPE = dna
LATESTGP        = Monodelphis_domestica.BROADO2.dec.dna.contig.fa
LATESTGP_MASKED = Monodelphis_domestica.BROADO2.dec.dna_rm.contig.fa
CDNA_ALL        = Monodelphis_domestica.BROADO2.dec.cdna.fa
CDNA_NOVEL      = Monodelphis_domestica.BROADO2.dec.cdna.novel.fa
CDNA_ABINITIO   = Monodelphis_domestica.BROADO2.dec.pep.abinitio.fa

[TBLASTX_DATASOURCES]
# Sequence databases to use with search method (TBLASTX)
# Filesystem location set by DEFAULTS:ENSEMBL_BLAST_DATA_PATH
# Data available from ftp://ftp.ensembl.org/pub/current_mouse/data/fasta/
DATASOURCE_TYPE = dna
LATESTGP        =  Monodelphis_domestica.BROADO2.dec.dna.contig.fa
LATESTGP_MASKED =  Monodelphis_domestica.BROADO2.dec.dna_rm.contig.fa
CDNA_ALL        = Monodelphis_domestica.BROADO2.dec.cdna.fa
CDNA_NOVEL      = Monodelphis_domestica.BROADO2.dec.cdna.novel.fa
CDNA_ABINITIO   = Monodelphis_domestica.BROADO2.dec.cdna.abinitio.fa

[TBLASTN_DATASOURCES]
# Sequence databases to use with search method (TBLASTN)
# Filesystem location set by DEFAULTS:ENSEMBL_BLAST_DATA_PATH
# Data available from ftp://ftp.ensembl.org/pub/current_mouse/data/fasta/
DATASOURCE_TYPE = peptide
LATESTGP        =  Monodelphis_domestica.BROADO2.dec.dna.contig.fa
LATESTGP_MASKED =  Monodelphis_domestica.BROADO2.dec.dna_rm.contig.fa
CDNA_ALL        = Monodelphis_domestica.BROADO2.dec.cdna.fa
CDNA_NOVEL      = Monodelphis_domestica.BROADO2.dec.cdna.novel.fa
CDNA_ABINITIO   = Monodelphis_domestica.BROADO2.dec.cdna.abinitio.fa

[BLASTP_DATASOURCES]
# Sequence databases to use with search method (BLASTP)
# Filesystem location set by DEFAULTS:ENSEMBL_BLAST_DATA_PATH
# Data available from ftp://ftp.ensembl.org/pub/current_mouse/data/fasta/
DATASOURCE_TYPE = peptide
PEP_ABINITIO    = Monodelphis_domestica.BROADO2.dec.pep.abinitio.fa
PEP_ALL         = Monodelphis_domestica.BROADO2.dec.pep.fa
PEP_NOVEL       = Monodelphis_domestica.BROADO2.dec.pep.novel.fa

[BLASTX_DATASOURCES]
# Sequence databases to use with search method (BLASTX)
# Filesystem location set by DEFAULTS:ENSEMBL_BLAST_DATA_PATH
# Data available from ftp://ftp.ensembl.org/pub/current_mouse/data/fasta/
DATASOURCE_TYPE = dna
PEP_ABINITIO    = Monodelphis_domestica.BROADO2.dec.pep.abinitio.fa
PEP_ALL         = Monodelphis_domestica.BROADO2.dec.pep.fa
PEP_NOVEL       = Monodelphis_domestica.BROADO2.dec.pep.novel.fa

####################
# Configure search example links
####################

                                                                                



[SEARCH_LINKS]<commit_msg>updated blast ssaha servers<commit_after>###############################################################################
#   
#   Name:           Monodelphis_domestica.ini
#   
#   Description:    Configuration file for Opossum Ensembl
#
###############################################################################

#################
# GENERAL CONFIG
#################
[general]

# Database info: only specify values if different from those in DEFAULTS

ENSEMBL_PREDICTION_TEXT_CORE    = Gene structures annotated by a preliminary run of the Ensembl annotation pipeline, only using GeneWise models generated from alignments of proteins from Uniprot. The models have been filtered to form non-redundant sets of transcripts for each gene.
ENSEMBL_SEARCH_IDXS = [ Domain Gene GenomicAlignment Marker Sequence ]

# Assembly info
ENSEMBL_PREFIX       = ENSMDO

ASSEMBLY_ID          = MonDom 2.0
ENSEMBL_GOLDEN_PATH  = BROADO2
ASSEMBLY_DATE        = 2005-05

GENEBUILD_BY         = Ensembl
GENEBUILD_DATE       = 2005-10
SPECIES_RELEASE_VERSION = 2

ENSEMBL_CHROMOSOMES  = []

# Search config
ENSEMBL_SEARCH_IDXS = [  Domain Family Gene GenomicAlignment Marker Sequence ]

# Das
#ENSEMBL_DAS_MAPMASTER_DSN = ;DAS mapmaster for "uploadable DAS"

ENSEMBL_BUM = Scaffold

# Display info
SPECIES_COMMON_NAME  = Opossum
SPECIES_BIO_NAME     = Monodelphis domestica
SPECIES_DESCRIPTION  = opossum
SPECIES_CODE         = md
SPECIES_GROUP        = Mammals
GENERATE_HOME_PAGE   = yes
CYTOVIEW_ENABLED     = 1

##################
# DATABASE CONFIG
# Change the values to the local names of these databases
##################

[databases]
ENSEMBL_DB      = %_core_%

# You can overide the default settings (in DEFAULTS.ini) for specific
# databases. To do this, create an ini-file for this species e.g.
# public-plugins/mirror/conf/ini-file/Monodelphis_domestica.ini with
# the section you wish to overwrite (see the example INI file:
# public-plugins/mirror/conf/ini-files/Genus_species.ini

####################
# Help Database Config
####################

[ENSEMBL_HELP] 
# Accept defaults


####################
# Species-specific colours
####################

[ENSEMBL_STYLE]

[ENSEMBL_COLOURS] 
# Accept defaults


####################
# External Database ad Indexer Config
####################

[ENSEMBL_EXTERNAL_DATABASES]
# Accept defaults

[ENSEMBL_EXTERNAL_INDEXERS]
# Accept defaults


#############
# DAS CONFIG
#############

[ENSEMBL_INTERNAL_DAS_SOURCES]

[PDB_Spice]

[Phenotypes]

# None


####################
# Configure External Genome Browsers
####################

[EXTERNAL_GENOME_BROWSERS] 
# None

####################
# Configure External URLs
# These are mainly for (1) External Genome Browse  {EGB_ }
#                      (2) DAS tracks              {DAS_ }
####################

[ENSEMBL_EXTERNAL_URLS]

####################
# Configure blast data sources. 
# Used in blastview to generate database dropdown
####################
[ENSEMBL_BLAST_METHODS]
# Registers blast methods. Key values are the
# Bio::Tools::Run::Search classes used to run the search 
# Accept defaults

[BLAST_DATASOURCES]
# Registers blast datasources. Key values are used as labels.
# Keys should be registered against methods in species.ini files
# Accept defaults


####################
# Configure search example links
####################


[SEARCH_LINKS]
{'fraction_non_alphanumeric': 0.17210746013057904, 'fraction_numerical': 0.006314888151557316, 'mean_word_length': 4.588516746411483, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 3, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '7652456', 'n_tokens_mistral': 3251, 'n_tokens_neox': 3041, 'n_words': 696}