GHOSTZ is a homology search tool which can detect remote homologues like BLAST and is about 200 times more efficient than BLAST by using database subsequence clustering. GHOSTZ outputs search results in the format similar to BLAST-tabular format.
$ tar xvzf ghostz.tar.gz
$ cd ghostz
$ make
$ cp ghostz /AS/YOU/LIKE/
GHOSTZ 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 format database files by using
GHOSTZ "db" command at first.
GHOSTZ"db" command requires 2 args ([-i dbFastaFile] and [-o dbName]).
GHOSTZ "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 "aln" command is used and that command
requires at least 2 args([-i qryName] and [-d dbName]).
$ ghostz db -i ./db.fasta -o exdb $ ghostz aln -i exqry -d exdb -o exout
db: convert a FASTA file to GHOSTX format database files
ghostz 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 aln [-i queries] [-o output] [-d database] [-v maxNumAliSub]
[-b maxNumAliQue] [-h hitsSize] [-l queriesChunkSize] [-q queryType]
[-t databaseType] [-F filter] [-a numThreads]
Options:
(Required)
-i STR DNA or protein sequences in FASTA format for queries
-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]
-n INT Minimum length of query in amino acid residues [12]
GHOSTZ 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
If the input is massive sequences and each sequence is extremely short, the program may terminate abnormally because of bad allocation. Try setting smaller chunk size of the queries or splitting input file.