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
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