User guide

The interface of G-BLASTN is almost identical to the original NCBI-BLAST with the following additional options: <br>

*** GPU options <br> -use_gpu <true|false> <br> Use 'true' to enable GPU for gblastn<br> Default = 'false'<br> -mode <1|2><br> 1.normal mode, 2.pipeline mode <br> Default = `1'<br> -query_list <br> The file includes the list of files names of your query files.<br>

IV. Example:<br>

1. In the work directory, we can make some sub-directories: <br> .<br> ├── bin<br> │   ├── blastn # the orignal blastn<br> │   └── gblastn # the G-BLASTN (you need to copy the compiled binary "blastn" into this direcotry, and rename to "gblastn" or others; <br> ├── blast<br> │   └── src<br> │   └── gpu<br> │      ├── c++<br> │      ├── install<br> │      ├── log<br> │      ├── ncbi-blast-2.2.28+-src<br> │   └── 2.28.zip<br> ├── data # NCBI nt database<br> │   └── nt2m<br> │      ├── nohup.out<br> │      ├── nt.2m.00.nhr<br> │      ├── ...<br> │      ├── nt.2m.counts<br> │      └── nt.2m.nal<br> ├── database # human and mouse database<br> │   └── blastdb<br> │   ├── human<br> │   │   ├── human.1-8.wm.body<br> │   │   ├── ...<br> │   │   ├── human.9-Y.wm.nsq<br> │   │   └── human.wm.nal<br> │   └── mouse<br> │   ├── mouse.1-10.wm.nhr<br> │   ├── ...<br> │   ├── mouse.11-Y.wm.nsq<br> │   ├── mouse.nal<br> │   └── mouse.wm.nal<br> ├── output # output directory<br> │   ├── query.101.fa.out<br> │   └── ...<br> ├── query # query directory<br> │   ├── queries<br> │   │   ├── human<br> │   │   │   ├── qlarge<br> │   │   │   │   ├── query.11.fa<br> │   │   │   │   └── ...<br> │   │   │   ├── qmedium<br> │   │   │   │   ├── query.100.fa<br> │   │   │   │   └── ...<br> │   │   │   └── qsmall<br> │   │   │   ├── query.101.fa<br> │   │   │   └── ...<br> │   │   └── mouse<br> │   │   ├── qlarge<br> │   │   │   ├── query.201.fa<br> │   │   │   └── ...<br> │   │   ├── qmedium<br> │   │   │   ├── query.101.fa<br> │   │   │   └── ...<br> │   │   └── qsmall<br> │   │   ├── query.100.fa<br> │   │   └── ...<br> │   └── SRR955707<br> │   ├── 1.fa<br> │   └── ...<br> ├── script # shell directory<br> │   └── new_query_human_mouse<br> │      ├── g.m.sh <br> │      └── m.ls<br> └── wm_counts # mask database for human and mouse<br> ├── human.stat<br> └── mouse.stat<br>

2. The shell of g.m.sh<br>

################################################################################################################### #!/bin/sh<br> echo "***************start*****************"<br> blastn="/home/blastn/bin/gblastn"<br> data_dir="/home/blastn/"<br> database="${data_dir}database/blastdb/mouse/mouse.wm"<br> maskdb="${data_dir}wm_counts/mouse.stat"<br> query_list="m.ls"<br> outpath="/home/blastn/output/log.txt"<br>

$blastn -db $database -window_masker_db $maskdb -query_list $query_list -outfmt "7" -out $outpath -use_gpu true<br>

echo "***************complete*****************" ###################################################################################################################

3. The m.ls file contains the path names of all your queries, e.g.:<br>

/home/blastn/query/queries/mouse/qmedium/query.195.fa<br> /home/blastn/query/queries/mouse/qmedium/query.130.fa