amin-jabri / ghostz-gpu

GHOSTZ-GPU

GHOSTZ-GPU is a homology search tool which can detect remote homologues like BLAST and is about 5-7 times more efficient than GHOSTZ by using GHOSTZ.

GHOSTZ-GPU outputs search results in the format similar to BLAST-tabular format.

Requirements

• gcc => 4.3
• Boost >= 1.55.0
• CUDA >= 6.0

Installation

1. Download the archive of GHOSTZ-GPU from this repository.
2. Extract the archive and cd into the extracted directory.
3. Run make command.
4. Copy ghostz-gpu binary file to any directory you like.

Commands:

$ tar xvzf ghostz-gpu.tar.gz
$ cd ghostz-gpu
$ make BOOST_PATH=Boost CUDA_TOOLKIT_PATH=CUDA
$ cp ghostz-gpu /AS/YOU/LIKE/

Boost and CUDA are directories where they are installed, respectively.

Usage

GHOSTZ-GPU requires specifically formatted database files for homology search. These files can be generated from FASTA formatted DNA/protein sequence files.

Users have to prepare a database file in FASTA format and convert it into GHOSTZ-GPU format database files by using GHOSTZ-GPU db command at first. GHOSTZ-GPU db command requires 2 args ([-i dbFastaFile] and [-o dbName]). GHOSTZ-GPU db command divides a database FASTA file into several database chunks and generates several files (.inf, .ind, .nam, .pos, .seq). All generated files are needed for the search. Users can specify the size of each chunk. Smaller chunk size requires smaller memory, but efficiency of the search will decrease.
For executing homology search, GHOSTZ-GPU aln command is used and that command requires at least 2 args ([-i qryName] and [-d dbName]).

Example

$ ghostz-gpu db  -i ./data/db.fasta -o exdb


$ ghostz-gpu aln -i ./data/queries.fasta -d exdb -o exout

Command and Options

db: convert a FASTA file to GHOSTZ format database files

ghostz-gpu db [-i dbFastaFile] [-o dbName] [-C clustering][-l chunkSize]
    [-L clusteringSubsequenceLength]  [-s seedThreshold]
Options:
(Required)
  -i STR    Protein sequences in FASTA format for a database
  -o STR    The name of the database
(Optional)
  -C STR    Clustering, T (enable) or F (disable) [T]
  -l INT    Chunk size of the database (bytes) [1073741824 (=1GB)]
  -L INT    Length of a subsequence for clustering [10]
  -s INT    The seed threshold [39]

aln: Search homologues of queries from database

ghostz-gpu aln [-i queries] [-o output] [-d database] [-v maxNumAliSub]
  [-b maxNumAliQue] [-h hitsSize] [-l queriesChunkSize] [-q queryType]
  [-t databaseType] [-F filter] [-a numThreads] [-g numGPUs]
Options:
(Required)
  -i STR    Sequences in FASTA format
  -o STR    Output file
  -d STR    database name (must be formatted)
(Optional)
  -v INT    Maximum number of alignments for each subject [1]
  -b INT    Maximum number of the output for a query [10]
  -l INT    Chunk size of the queries (bytes) [134217728 (=128MB)]
  -q STR    Query sequence type, p (protein) or d (dna) [p]
  -t STR    Database sequence type, p (protein) or d (dna) [p]
  -F STR    Filter query sequence, T (enable) or F (disable) [T] 
  -a INT    The number of threads [1]
  -g INT    The number of GPUs [the number of available GPUs]

Search results

GHOSTZ-GPU outputs the tab-deliminated file as search results.

Example)

hsa:124045...   hsa:124045...   100       139     0       0       1       139     1       139     2.04391e-76     283.878
hsa:124045...   ptr:454320...   99.2126        127     1       0       13      139     14      140     5.96068e-68     255.758
hsa:124045...   mcc:714360...   88.9764        127     14      0       13      139     14      140     5.05773e-59     226.098
hsa:124045...   rno:292078...   58.6777        121     46      2       13      133     14      130     1.38697e-32     138.272
hsa:124045...   mmu:320869...   55.9055        127     50      3       13      139     12      132     1.17414e-31     135.191
hsa:124045...   pon:100434...   96.4912        57      2       0       13      69      14      70      3.65839e-25     113.62
hsa:124045...   bta:100335...   44.9275        138     71      3       2       139     25      157     4.04482e-24     110.153
hsa:124045...   aml:100464...   26.6667        75      46      2       13      81      1183    1254    0.820692        32.7278
hsa:124045...   bfo:BRAFLD...   56    25      10      1       108     131     581     605     0.820692        32.7278
hsa:124045...   tgu:100227...   26.1682        107     69      3       25      130     150     247     1.82831 31.5722

Each column shows;

1. Name of a query sequence
2. Name of a homologue sequence (subject)
3. Sequence Identity
4. Alignment length
5. The number of mismatches in the alignment
6. The number of gap openingsin the alignemt
7. Start position of the query in the alignment
8. End position of the query in the alignemnt
9. Start position of the subject in the alignment
10. End position of the subject in the alignment
11. E-value
12. Normalized score

References

Shuji Suzuki, Masanori Kakuta, Takashi Ishida, Yutaka Akiyama. Acceleration of sequence homology searches by means of graphics processing units (GPUs) and database subsequence clustering. (submitted)

Copyright © 2015 Akiyama_Laboratory, Tokyo Institute of Technology, All Rights Reserved.