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$parse_protein_id.pl
SeqID before parse: >g18373.t1|PACid:27562759
SeqID after parse : >g18373.t1
*Important*
After that, please add Rice and Arabidopsis output to your folder for making clusters.
For some species, using PACid is better than using original transcript ID
B. Create a list for plant peptide and CDS sequences. The format of the list is like below:
Each line include five columns, they are:
A: folder for species (rice)
B: monocotyledon / dicotyledon / non-angiosperms
C: Name of plant species
The protein, CDS and other files are named according to A: folder for species
A: CDS sequence -- rice_cds
B: protein -- rice_pep
C: representive protein -- rice_rep_pep (optional)
D: protein & transcirpt & gene file -- rice_trans_gene
E: gene position file -- rice_gene_position (optional)
F: chr Size file -- rice_chrSize (optional)
G: block file -- rice_block (optional)
H: Other block file -- rice_other_block (optional)
Example:
A: publishedPlantGenome/rice
B: monocotyledon
C: Rice
Below info do not have order
A: publishedPlantGenome/rice/rice_cds
B: publishedPlantGenome/rice/rice_pep
C: publishedPlantGenome/rice/rice_rep_pep
D: publishedPlantGenome/rice/rice_trans_gene
E: publishedPlantGenome/rice/rice_gene_position
F: publishedPlantGenome/rice/rice_chrSize
G: publishedPlantGenome/rice/rice_block
H: publishedPlantGenome/rice/rice_other_block
* other in H should be name of other species
Each line of protein & transcirpt & gene file include three columns:
A: protein ID
B: transcript ID
C: gene ID
Each line of gene position file:
A: chrID
B: start
C: end
E: strand
F: geneID/mRNA
Each line of chr Size file
A: chrID
B: chrName
C: length
D: color
C. run iTAK.
Command or make a bash for each specie:
$perl /path/iTAK.pl -i apple_pep
Input:
The peptide sequence
Output:
Each plant species will generates one output folder in publishedPlantGenome folder, and each folder will have 6 files:
apple_pep_pkaln : alignment of protein kinase
apple_pep_pkcat : assign each gene to different PK families
apple_pep_pkseq : protein kinase sequences
apple_pep_tf_align : alignment of transcription factor
apple_pep_tf_family : assign each gene to TF families
apple_pep_tf_seq : TF sequences
D. generate file for updating iTAK database
$perl itak_DB_update.pl list
Input:
The list created in step 1.
Output:
The output includes files that categorized to five parts (folders) for iTAK databases.
1. for_database -- include files that need to imported to mysql database
category
family_summary
protein_domain_table
protein_family_table
gene_table
*protein_annotation (generated at step 5)
2. for_download -- include files that could be download from the iTAK website
All_PKs_list
All_PKs_protein
All_TFs_TRs_nucleotide
All_PKs_nucleotide
All_TFs_TRs_list
All_TFs_TRs_protein
protein_kinases [folder]
transcription_factors_and_transcriptional_regulators [folder]
3. for_blast -- include files that need to be blast online, and gene annotation
All_PKs_nucleotide
All_PKs_protein
All_TFs_TRs_nucleotide
All_TFs_TRs_protein
4. for_cluster / for_tree -- include nwk files generated by clustalW2
5. for_synteny -- include gene list for synteny analysis
E. Blast protein sequence against Genebank for annotation
1. prepare the protein sequence for blast
$perl iTAK_DB_prepare_blast.pl pre_TFs_proteins pre_PKs_proteins new_TFs_proteins new_PKs_proteins
* the output file is Prepared_Protein.fa
2. upload protein sequence to codequest Server
3. parse the blast result:
$perl iTAK_DB_parse_blast.pl blast_results > update_protein_annotation_version
* the output file is protein_annotation_table file for importing to database
command for import these files to database:
LOAD DATA LOCAL INFILE 'family_summary' INTO TABLE `family` FIELDS TERMINATED BY '\t' ESCAPED BY '\\' LINES TERMINATED BY '\n';
Here is the command for importing each table:
mysql> truncate table itak.category;
mysql> load data local infile "/var/www/cgi-bin/itak/mysql_database/versionN/category" into table itak.categroy;
mysql> truncate table itak.gene;
mysql> load data local infile "/var/www/cgi-bin/itak/mysql_database/versionN/gene_table" into table itak.gene;
mysql> truncate table itak.family_summary;
mysql> load data local infile "/var/www/cgi-bin/itak/mysql_database/versionN/family_summary" into table itak.family_summary;
mysql> truncate table itak.gene_domain;
mysql> load data local infile "/var/www/cgi-bin/itak/mysql_database/versionN/protein_domain_table" into table itak.gene_domain;
mysql> truncate table itak.gene_family;
mysql> load data local infile "/var/www/cgi-bin/itak/mysql_database/versionN/protein_family_table" into table itak.gene_family;
** mysql> truncate table itak.gene_annotation; (do not need truncate this table)
mysql> load data local infile "/var/www/cgi-bin/itak/mysql_database/versionN/update_protein_annotation_version" into table itak.gene_annotation;
Problem: some genes assigned to both PKs and TFs families: please check gene_family table
H. Format the database
Using formatdb command to format the blast files
$formatdb -i All_PKs_nucleotide -p F
$formatdb -i All_PKs_protein -p T
$formatdb -i All_TFs_TRs_nucleotide -p F
$formatdb -i All_TFs_TRs_protein -p T
G. Update webpage
1. db_home.cgi
add plant info to data hash
add plant name to tree base on http://genomevolution.org/wiki/index.php/Sequenced_plant_genomes
Ref: Generate and Draw phylogenetic tree automatically
A. Generate phylogenetic tree using MEGA
1. using MEGA-CC can generate phylogenetic tree automatically
(http://update.megasoftware.net/download.php?email=yz357@cornell.edu&location=primary&version=win-5.1CC)
(http://www.megasoftware.net/download.php?email=yz357@cornell.edu&location=secondary&version=win-5.1CC)
B. Draw phylogenetic tree
1. convert newick format to phyloXML format using forester_1019.jar (http://code.google.com/p/forester/)
2. display phyloXML using jsPhyloSVG (http://www.jsphylosvg.com/)
*using perl to construct the pipeline
*about phyloxml (http://www.phyloxml.org/), including many tools to display the trees.
Ref: Parameters for Blast
For your iTAK protein blast, can you tell me what parameters you want to use, specifically
"Max Scores"
"Max Alignments"
"Significance Threshold"
http://132.236.156.152/decypher/algo-tera-blast/tera-blastp_aa.shtml
Ref: How to backup/install iTAK database on a different computer
Before backup/install, your destination computer already has apache and mysql installed.
Step1. Copy /var/www/html/tools/itak/ and /var/www/cgi-bin/itak/ folders from server to your destination computer.
Step2. Create itak database and import database file into it.
$ mysql -u root -p # enter mysql
mysql> create database itak; # create itak database
$ mysql -uroot -p itak< itak_db_stru.mysql; # import the structure of itak tables
# load dataset to itak tables
mysql> load data local infile "/var/www/cgi-bin/itak/mysql_database/versionN/category" into table itak.categroy;
mysql> load data local infile "/var/www/cgi-bin/itak/mysql_database/versionN/domain_table" into table itak.domain;
mysql> load data local infile "/var/www/cgi-bin/itak/mysql_database/versionN/family_table" into table itak.family;
mysql> load data local infile "/var/www/cgi-bin/itak/mysql_database/versionN/gene_table" into table itak.gene;
mysql> load data local infile "/var/www/cgi-bin/itak/mysql_database/versionN/family_summary" into table itak.family_summary;
mysql> load data local infile "/var/www/cgi-bin/itak/mysql_database/versionN/gene_domain_table" into table itak.gene_domain;
mysql> load data local infile "/var/www/cgi-bin/itak/mysql_database/versionN/gene_family_table" into table itak.gene_family;
mysql> load data local infile "/var/www/cgi-bin/itak/mysql_database/versionN/gene_annotation" into table itak.gene_annotation;
create user for itak database
mysql> create user itak;
mysql> grant select [insert, update, delete] on itak.* to itak@localhost identified by "itak"
Step3. Change the limit of folders and files using chmod command.
Step4. Edit the itak.pm base on the environment of destination computer.
our $tmp = "/var/www/html/tmp";
our $home = "/var/www/html/tool/itak";
our $ftp_url = "ftp://bioinfo.bti.cornell.edu/pub/program/itak";
our $http_url = "http://bioinfo.bti.cornell.edu/tool/itak";
our $root_url = "http://bioinfo.bti.cornell.edu";
* if you have any problem on mysql db, please check the mysql db card in Evernote
Ref: The structure of iTAK database
mysql> use database;
mysql> show tables;
+-----------------+
| Tables_in_itak |
+-----------------+
| domain |
| family |
| family_summary |
| gene |
| gene_annotation |
| gene_domain |
| gene_family |
+-----------------+
use the mysql command to show structure of tables:
mysql> desc category;
+----------+-------------+------+-----+---------+-------+
| Field | Type | Null | Key | Default | Extra |
+----------+-------------+------+-----+---------+-------+
| organism | varchar(50) | NO | MUL | NULL | |
| category | varchar(50) | NO | | NULL | |
+----------+-------------+------+-----+---------+-------+
mysql> desc domain;
+-------------+-------------+------+-----+---------+-------+
| Field | Type | Null | Key | Default | Extra |
+-------------+-------------+------+-----+---------+-------+
| domain_ID | varchar(15) | NO | PRI | NULL | |
| domain_desc | text | YES | | NULL | |
| category | varchar(15) | YES | | NULL | |
+-------------+-------------+------+-----+---------+-------+
This table do not need update!!!
mysql> desc family;
+-------------+--------------+------+-----+---------+-------+
| Field | Type | Null | Key | Default | Extra |
+-------------+--------------+------+-----+---------+-------+
| family_acc | varchar(25) | NO | PRI | NULL | |
| description | varchar(255) | YES | | NULL | |
| category | varchar(50) | YES | | NULL | |
+-------------+--------------+------+-----+---------+-------+
This table do not need update!!!
mysql> desc family_summary;
+-------------+-------------+------+-----+---------+-------+
| Field | Type | Null | Key | Default | Extra |
+-------------+-------------+------+-----+---------+-------+
| family_acc | varchar(25) | NO | PRI | NULL | |
| Number_gene | smallint(6) | YES | | NULL | |
| organism | varchar(50) | NO | PRI | NULL | |
+-------------+-------------+------+-----+---------+-------+
mysql> desc gene;
+-------------+-------------+------+-----+---------+-------+
| Field | Type | Null | Key | Default | Extra |
+-------------+-------------+------+-----+---------+-------+
| gene_ID | varchar(50) | NO | PRI | NULL | |
| protein_seq | text | YES | | NULL | |
| CDS_seq | text | YES | | NULL | |
| organism | varchar(50) | NO | PRI | | |
+-------------+-------------+------+-----+---------+-------+
mysql> desc gene_annotation;
+-------------+-------------+------+-----+---------+-------+
| Field | Type | Null | Key | Default | Extra |
+-------------+-------------+------+-----+---------+-------+
| trans_ID | varchar(50) | NO | PRI | NULL | |
| gene_ID | varchar(50) | NO | | NULL | |
| protein_seq | text | YES | | NULL | |
| CDS_seq | text | YES | | NULL | |
| organism | varchar(50) | NO | PRI | | |
+-------------+-------------+------+-----+---------+-------+
+----------+-------------+------+-----+---------+-------+
| Field | Type | Null | Key | Default | Extra |
+----------+-------------+------+-----+---------+-------+
| gene_ID | varchar(50) | NO | PRI | NULL | |
| hit_acc | varchar(50) | NO | PRI | NULL | |
| hit_desc | text | NO | | NULL | |
| score | float | NO | | NULL | |
| evalue | varchar(10) | NO | | NULL | |
+----------+-------------+------+-----+---------+-------+
mysql> desc gene_domain;
+--------------+-------------+------+-----+---------+-------+
| Field | Type | Null | Key | Default | Extra |
+--------------+-------------+------+-----+---------+-------+
| gene_ID | varchar(50) | NO | PRI | | |
| domain_ID | varchar(50) | NO | PRI | | |
| query_start | smallint(6) | NO | PRI | 0 | |
| query_end | smallint(6) | NO | PRI | 0 | |
| target_start | smallint(6) | YES | | NULL | |
| target_end | smallint(6) | YES | | NULL | |
| align_query | text | YES | | NULL | |
| align_string | text | YES | | NULL | |
| align_hit | text | YES | | NULL | |
| score | float | YES | | NULL | |
| evalue | varchar(10) | YES | | NULL | |
+--------------+-------------+------+-----+---------+-------+
mysql> desc gene_family;
+------------+-------------+------+-----+---------+-------+
| Field | Type | Null | Key | Default | Extra |
+------------+-------------+------+-----+---------+-------+
| gene_ID | varchar(50) | NO | PRI | NULL | |
| family_acc | varchar(25) | NO | PRI | NULL | |
+------------+-------------+------+-----+---------+-------+