Due to web problem, please visit the server at http://cefg.uestc.cn:81/CasLocusAnno/index.html temporarily
python 2.7+ https://www.python.org/download/releases/2.7/
Biopython https://biopython.org/wiki/Download
psiblast ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.7.1/
makeblastdb ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.7.1/
mcl http://micans.org/mcl/
The bin folder has already included all the required programs
Please always keep the required programs in the bin folder of CasLocusAnno
Make sure you have the permission to execute the required programs before running CasLocusAnno.py
Command:
python CasLocusAnno.pyc -i <inputFile> -o <OutFile>
Options:
-h, --help Check help of CasLocusAnno.py
-v, --version Check the current release version
-i, --input Input file (Whole proteome sequences)
-o, --out Output file of result
-i, -o are required parameters.
The code can be copiable, distributable, modifiable, and usable without any restrictions.
Report bugs to <chuand@cefg.cn> or <fbguo@uestc.edu.cn>
CasLocusAnno Main file
├── bin
├── CasLocusAnno.py Main program
├── configure
│ └── profile.ini Profile information
├── profiles Cas profile
├── readme
├── temp A temporary file that stores data during the annotation procedure
└── test File that stores test data and their annotation result
├── NC_015709.faa
├── res
├── res.anno1
└── res.anno2
The standalone version only accepts whole proteome sequence of a chromosome.
All the sequences in the inputting file should in the order that they appear in chromosome.
<OutFile>.anno1 Cas protein list in the first-round search
<OutFile>.anno2 Cas protein list in the second-round search
<OutFile> Cas proteins in Cas loci and (sub)types
An example of <OutFile>. The following annotation comes from NC_015709, which is downloaded from
ftp://ftp.ncbi.nlm.nih.gov/genomes/archive/old_refseq/Bacteria/Zymomonas_mobilis_pomaceae_ATCC_29192_uid68445/NC_015709.faa
Cas locus type: No Cas locus
=====
1001 gi|338707994|ref|YP_004662195.1| 7.32e-43 pfam09707.sr cas2 cas2 CAS-I-E
1002 gi|338707995|ref|YP_004662196.1| 3.02e-132 cd09719.sr cas1 cas1 CAS-I-E
1003 gi|338707996|ref|YP_004662197.1| 9.04e-37 pfam08798.sr cas6e cas6e CAS-I-E,CAS-IV
1004 gi|338707997|ref|YP_004662198.1| 3.58e-35 cd09645.sr cas5 cas5 CAS-I-E
1005 gi|338707998|ref|YP_004662199.1| 2.91e-115 pfam09344.sr cas7 cas7 CAS-I-E
1006 gi|338707999|ref|YP_004662200.1| 9.69e-20 cd09731.sr cse2gr11 cse2gr11 CAS-I-E
1007 gi|338708000|ref|YP_004662201.1| 3.8e-83 cd09729.sr cas8e cas8e CAS-I-E
1008 gi|338708001|ref|YP_004662202.1| 3.31e-64 COG1203.sr cas3 cas3 CAS-I
1008 gi|338708001|ref|YP_004662202.1| 2.05e-21 cd09641.sr cas3HD cas3HD CAS-I
Cas locus type: CAS-I-E
=====
Cas locus type: No Cas locus
=====
Cas locus type: No Cas locus
=====
We used MCCS further to filter the initial annotation,
Cas proteins that may not constitute a Cas locus or may be false discovery were discarded.
This is the reason why you see "Cas locus type: No Cas locus".
There is one Cas locus belonging to CAS-I-E in the chromosome