dbCAN：CAZyme序列和注释数据库

文献信息：

标题：dbCAN-seq: a database of carbohydrate-active enzyme (CAZyme) sequence and annotation
中文：碳水化合物酶序列注释数据库dbcan-seq
杂志：Nucleic Acids Research
时间：2018
单位：北伊利诺斯大学，南开大学

meta server：http://bcb.unl.edu/dbCAN2/
dbcan_seq：http://bcb.unl.edu/dbCAN_seq/help.php
dbcan_seq DB：http://bcb.unl.edu/dbCAN_seq/download.php
dbcan github：https://github.com/linnabrown/run_dbcan

难道还能注释转录因子和转运体，还有碳水化合物酶基因簇？？？

下载安装

conda create -n run_dbcan python=3.8 diamond hmmer prodigal -c conda-forge -c bioconda
conda activate run_dbcan
pip install dbcan==3.0.5

下载注释信息和建库

test -d db || mkdir db
cd db \
    && wget http://bcb.unl.edu/dbCAN2/download/CAZyDB.09242021.fa && diamond makedb --in CAZyDB.09242021.fa -d CAZy \
    && wget https://bcb.unl.edu/dbCAN2/download/Databases/V10/dbCAN-HMMdb-V10.txt && mv dbCAN-HMMdb-V10.txt dbCAN.txt && hmmpress dbCAN.txt \
    && wget http://bcb.unl.edu/dbCAN2/download/Databases/tcdb.fa && diamond makedb --in tcdb.fa -d tcdb \
    && wget http://bcb.unl.edu/dbCAN2/download/Databases/tf-1.hmm && hmmpress tf-1.hmm \
    && wget http://bcb.unl.edu/dbCAN2/download/Databases/tf-2.hmm && hmmpress tf-2.hmm \
    && wget http://bcb.unl.edu/dbCAN2/download/Databases/stp.hmm && hmmpress stp.hmm \
    && cd ../ && wget http://bcb.unl.edu/dbCAN2/download/Samples/EscheriaColiK12MG1655.fna \
    && wget http://bcb.unl.edu/dbCAN2/download/Samples/EscheriaColiK12MG1655.faa \
    && wget http://bcb.unl.edu/dbCAN2/download/Samples/EscheriaColiK12MG1655.gff

后台下载

nohup bash down.sh &

运行run_dbcan

run_dbcan EscheriaColiK12MG1655.fna prok \
--db_dir /public/home/zzumgg03/huty/databases/dbcan/ \
--out_dir output_EscheriaColiK12MG1655

参数：
--dia_eval DIAMOND E Value
--dia_cpu Number of CPU cores that DIAMOND is allowed to use
--hmm_eval HMMER E Value
--hmm_cov HMMER Coverage val
--hmm_cpu Number of CPU cores that HMMER is allowed to use
--out_pre Output files prefix
--out_dir Output directory
--db_dir Database directory

过程

***************************1. DIAMOND start****

diamond v2.0.15.153 (C) Max Planck Society for the Advancement of Science
Documentation, support and updates available at http://www.diamondsearch.org
Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021)

#CPU threads: 4
Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1)
Temporary directory: output_EscheriaColiK12MG1655
#Target sequences to report alignments for: 1
Opening the database...  [0.253s]
Database: /public/home/zzumgg03/huty/databases/dbcan/CAZy.dmnd (type: Diamond database, sequences: 2161786, letters: 1024499689)
Block size = 2000000000
Opening the input file...  [0.001s]
Opening the output file...  [0.001s]
Loading query sequences...  [0.011s]
Masking queries...  [0.066s]
Building query seed set...  [0.193s]
Algorithm: Query-indexed
Building query histograms...  [0.007s]
Allocating buffers...  [0s]
Loading reference sequences...  [3.197s]
Initializing temporary storage...  [0.092s]
Building reference histograms...  [19.495s]
Allocating buffers...  [0.001s]
Processing query block 1, reference block 1/1, shape 1/2.
Building reference seed array...  [11.985s]
Building query seed array...  [0.053s]
Computing hash join...  [1.719s]
Searching alignments...  [10.015s]
Processing query block 1, reference block 1/1, shape 2/2.
Building reference seed array...  [11.761s]
Building query seed array...  [0.037s]
Computing hash join...  [1.702s]
Searching alignments...  [13.334s]
Deallocating buffers...  [0.208s]
Clearing query masking...  [0.002s]
Computing alignments...  [42.04s]
Deallocating reference...  [0.067s]
Loading reference sequences...  [0.028s]
Deallocating buffers...  [0.001s]
Deallocating queries...  [0s]
Loading query sequences...  [0.003s]
Closing the input file...  [0s]
Closing the output file...  [0.001s]
Cleaning up...  [0s]
Total time = 117.041s
Reported 197 pairwise alignments, 197 HSPs.
197 queries aligned.

***************************1. DIAMOND end****
***************************2. HMMER start***
***************************2. HMMER end***
***************************3. eCAMI start****
Using CAZyme db in eCAMI
total time:2642.618377s
***************************3. eCAMI end****

Preparing overview table from hmmer, eCAMI and diamond output...
overview table complete. Saved as output_EscheriaColiK12MG1655/overview.txt

结果

安装信号肽预测工具signalp添加到系统环境（可选）

文献：SignalP 5.0 improves signal peptide predictions using deep neural networks. NBT 2019
signalp地址：https://services.healthtech.dtu.dk/
这里有很多工具，signalp在里面，下载安装没及时保存
使用方法：

signalp -org gram+ \
-batch 10000 \
-format long \
-fasta Result/prokka/genome_prokka.faa \
-prefix Result/secretory/signalp_pos/genome_signalp_pos \
-tmp $tmp

mkdir Result/secretory/signalp_neg
signalp -org gram- \
-batch 10000 \
-format long \
-fasta Result/prokka/genome_prokka.faa \
-prefix Result/secretory/signalp_neg/genome_signalp_neg \
-tmp $tmp