Temporarily available

Due to web problem, please visit the server at http://cefg.uestc.cn:81/CasLocusAnno/index.html temporarily

Requirements

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

Usage

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>

Directory structure

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

noting

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.

Output

<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