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Files produced by PyMood BLAST Launcher / Parser

Note: Numbers in this document with 'e' refer to exponents, for example, 2e-100 refers to 2 × 10-100.

To run BLAST, PyMood BLAST Launcher uses FASTA files. They may have different types of extensions. The most common ones are: .fasta, .faa (fasta amino acid), .ffn (fasta functional nucleotide), .pep, .cds (coding DNA sequence), and .seq. Here we supply as an example the fowlpox.faa file. These are the text files, and can be opened in a text editor.
Running BLAST comparisons on a desktop can take from a few minutes to many hours, depending on the size of FASTA files and the computer processor speed. For example, a comparison of 484 proteins of Mycoplasma genitalis against 689 proteins of Mycoplasma pneumonia takes less then a minute on a 1GHz processor. A comparison of 2267 proteins of Lactococcus lactis against 4279 proteins of Escherichia coli takes about 8 minutes, and comparison of the entire proteome of Arabidopsis thaliana vs. the entire proteome of human takes 18 hours on the same processor.



For every comparison, upon completion of BLAST run, PyMood BLAST Launcher / Parser will produce the following nine files :

.*blast*

The exact extension will correspond to the BLAST type selected (blastn, blastp, blastx, tblastn, or tblastx). An example would be: fowlpox_vs_monkeypox.blastp
These are the text files, and can be opened in a text editor.

.annotation

For both the query fasta file and the target fasta file, PyMood BLAST Launcher will produce FileName.annotation files. Examples are:
fowlpox.annotation and monkeypox.annotation
Each annotation file is a tab-delimited text file, consists of two columns and can be opened in a spreadsheet program or text editor. The first column contains the unique identifier for every gene, and the second column contains the gene name and/or annotation. Annotation in this file is extracted from the corresponding FASTA files.

.*blast*.matrix.subj.annotation

For each target fasta file, PyMood BLAST parser will produce a FileName.*blast*.matrix.subj.annotation file. An example is:
fowlpox_vs_monkeypox.blastp.matrix.subj.annotation
This annotation is extracted from the corresponding .blastp file and contains the annotation data for only those sequences from the target fasta file that are present in the BLAST output file. Each annotation file is a tab-delimited text file, consisting of two columns and can be opened in a spreadsheet program or text editor. The first column contains the unique identifier for every gene, and the second column contains the gene name and/or annotation.

.*blast*.matrix

For every BLAST output, PyMood BLAST parser will create a matrix file with the extension .matrix
An example given here is:
fowlpox_vs_monkeypox.blastp.matrix
This is a tab-delimited text file, and can be opened in a spreadsheet editor. The file contains eight columns, where:

A. unique identifier for the query gene
B. unique identifier of the best BLAST hit in the target FASTA file, if it is above the cutoff of the Expectation value set in BLAST Launcher
C. normalized1 expectation values
D. score (bits)
E. percentage of identity between the overlapping regions
F. number of identical letters in the overlap
G. length of the overlap
H. shows 1 if there is a BLAST hit found

1 normalized expectation value reflects the absolute value of the exponent in the expectation value. If the expectation value is 2e-15, the normalized expectation value is 15. For all expectation values better than e-100, like 3e-101, 7e-156, etc., the normalized expectation value 100 is assigned.

.*blast*.matrix.all_hits

Files with the extension .all_hits are tab-delimited text files, containing 14 columns with the results from BLAST output, and can be opened in a spreadsheet editor. An example here is:
fowlpox_vs_monkeypox.blastp.matrix.all_hits
The description of the columns: A. unique identifier for the query gene
B. unique identifiers of all BLAST hits in the target fasta file (above the cutoffs set in BLAST Launcher)
C. normalized expectation values for all hits
D. score (bits)
E. percentage of identity between overlapping regions
F. number of identical letters in the overlap
G. length of the overlap
H. order number of the hit for every query gene
I. assigns number 1 to every primary alignment1, assigns numbers 2, 3, 4, etc. to the alternative alignments2, if any
J. indicates if the alignment is primary, 'PRM' or alternative, 'ALT'
K. first position of the query sequence in the alignment
L. last position of the query sequence in the alignment
M. first position of the target sequence in the alignment
N. last position of the target sequence in the alignment

1 the alignment is primary when it is the best scored alignment between the query sequence and the particular target sequence
2 the alignment is alternative when it is not the best scored alignment between the query sequence and the particular target sequence

.*blast*.matrix.info1

An example here is: fowlpox_vs_monkeypox.blastp.matrix.info1
This is a tab-delimited text file, and can be opened in a spreadsheet editor. The file contains eight columns, where:

A. unique identifier for the query gene
B. unique identifier of the best BLAST hit in the target fasta file, if it is above the cutoff of the Expectation value set in BLAST Launcher
C. annotation of the best BLAST hit in the target fasta file
D. normalized1 expectation values
E. score (bits)
F. percentage of identity between the overlapping regions
G. number of identical letters in the overlap
H. length of the overlap
I. shows 1 if there is a BLAST hit found

1 normalized expectation value reflects the absolute value of the exponent in the expectation value. If the expectation value is 2e-15, the normalized expectation value is 15. For all expectation values better than e-100, like 3e-101, 7e-156, etc., the normalized expectation value 100 is assigned.

.*blast*.matrix.info2

An example here is: fowlpox_vs_monkeypox.blastp.matrix.info2
This is a tab-delimited text file, and can be opened in a spreadsheet editor. The file contains 13 columns with the results from BLAST output, where:

A. unique identifier for the query gene
B. unique identifiers of all BLAST hits in the target fasta file (above the cutoffs set in BLAST Launcher)
C. annotation of the BLAST hits
D. normalized1 expectation values
E. score (bits)
F. percentage of identity between overlapping regions
G. number of identical letters in the overlap
H. length of the overlap
I. order number of the hit for every query gene
J. first position of the query sequence in the alignment
K. last position of the query sequence in the alignment
L. first position of the target sequence in the alignment
M. last position of the target sequence in the alignment

1 normalized expectation value reflects the absolute value of the exponent in the expectation value. If the expectation value is 2e-15, the normalized expectation value is 15. For all expectation values better than e-100, like 3e-101, 7e-156, etc., the normalized expectation value 100 is assigned.

.*blast*.matrix.blast_stat

An example here is: fowlpox_vs_monkeypox.blastp.matrix.blast_stat
These tab-delimited text files contain a summary of BLAST output statistics. The files consist of three columns, and can be opened in a spreadsheet editor:

A. sequence order number
B. unique identifier for the query fasta file sequence
C. number of primary alignments in the BLAST file for the given query file sequence



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