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ACT Comparison File

My note on making the ACT comparison file. 1st Revison (May2, 2010) : Correction of grammatical mistakes. No more information added.

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somchais
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423 views

ACT Comparison File

My note on making the ACT comparison file. 1st Revison (May2, 2010) : Correction of grammatical mistakes. No more information added.

Uploaded by

somchais
Copyright
© Attribution Non-Commercial (BY-NC)
Available Formats
Download as PDF, TXT or read online on Scribd
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Note: ACT Comparison File

S. Saengamnatdej
April 28, 2010

My note on how to make a ACT comparison file.

1. Get your copy of a stand-alone version of BLAST (Windows XP or Linux) from the NCBI
website.
2. Both operation systems, use the same command lines. For Windows XP, run them in DOS
window and for Linux, in Xterminal window.
3. Download sequences in EMBL format from ebi genomes web page and save them with the
'embl' extension. (However, with SRS server, it can specify the sequence in fasta format.)
4. Use Artemis to write the embl format into fasta format (Load the file >>File>Write>All Bases >
FASTA format and save it with 'dna' extension).
5. In the directory containing the sequence files, designate one sequence as a database with the
following command. (then, press enter.)

formatdb -i seqA.dna -p F

(formatdb is a programme, -i is for input, -p designates the sequence type: F or DNA and T for
protein)

6. Run BLAST. Use blastall to run blastn, tblastx, blastp, or blastx by using an appropriate input
data file (DNA or Protein). Blastn and tblastx are suitable for generating ACT comparison files.
If very large sequences (several Mb) are being compared, megablast should be used instead of
blastall.
For running blastn in blastall use the following command: (then, press return.)

blastall -p blastn -m 8 -d seqA.dna -i seqB.dna -o seqA_vs_seqB

(tblastx can be used in place of blastn, blastall is the BLAST programme, -p specifies the type
of BLAST, - m 8 for the ACT readable output, -d for the database sequence, -i for the query
sequence, -o designates the name of the output file.)

7. The output file can now be used in ACT programme along with two dna and embl files.

8. In the case of larger files with high similarity, the megablast is preferred than blastall. It can
perform only DNA-DNA alignments (blastn), but not translated DNA-DNA alignments
(tblastx). Megablast is suit to comparing highly similar sequences such as the ones from the
same or very closely related species. Because the default output format from megablast is one
line per entry that ACT can read, there is no need to add '-m 8'. Therefore, the command will
look like this: (again, as the end of the command, press enter.)

megablast -d seqBigA.dna -i seqBigB.dna -o SeqBigA_vs_SeqBigB

Reference: The Wellcome Trust Manual of the Workshop on Working with Pathogenic Genomes.

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