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Old 11-06-2015, 02:26 PM   #1
mido1951
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Default blast final report

Hello,
I used BLASTn (blastn) and here are some of the output file.
I have some questions about the results. Thanks for answering me.
First, as you see I have alignment blocks, how can I have a total alignment without division into blocks (one block)?
and for e-value I put in the order 1E-10, why there are 273-2E, 4E-145, ...?
and according to you, the first results it is a good alignment?
thanks for your answer
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Old 11-06-2015, 03:29 PM   #2
mastal
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The smaller the E-values, the higher the alignment score, so those are your top hits.
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Old 11-07-2015, 04:07 AM   #3
mido1951
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thankyou
how can I have a total alignment without division into blocks (one block)?
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Old 11-07-2015, 04:25 AM   #4
GenoMax
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"L" in BLAST stands for "local".

BLAST is a local alignment algorithm and reports local alignments as HSP. If you want a "global" alignment then you need to use a different algorithm (e.g. Needleman-Wunsch). Since you have been posting about MinION data for a while you may not get a single block global alignment because of the differences evident in the query image you included.

Any two sequences can be aligned globally if one introduces enough gaps etc but it is important to keep in mind that such an alignment will not make any biological sense.
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Old 11-07-2015, 04:40 AM   #5
mido1951
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Thank you for your answer.
But you have not understood me.
as the figure shows there are two blocks and the second block is the alignment after the first block(it is the suite of the first block), just BLAST divides the alignments into Blocks and I looking for a solution for a single line without the division into blocks.
I hope that's clear.
Thank you
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Old 11-07-2015, 05:30 AM   #6
GenoMax
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If by "blocks" you mean that the alignment is printed on different lines (so it fits on a page) then that is how blast displays the alignments. This is traditionally done because of a need to fit these on a printed paper (blast is an "old' program compared to the web).

If you need the alignments to be on a single line you may have to use a pair-wise alignment program outside of blast or edit the blast output (it is plain text).
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Old 11-07-2015, 05:49 AM   #7
mido1951
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Yes, I want to have an alignment on a single line.
How to change the output file of Bast for this type of alignment because I have not found in --help Blast.
Or, you have other alignment tools in pairs to have this kind of results.
thanks
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Old 11-07-2015, 06:14 AM   #8
GenoMax
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You can't get that type of output with blast.

Is there a reason you want the alignment on one line? Do you need the query/hit aligned like blast?
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Old 11-07-2015, 06:20 AM   #9
mido1951
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I want to change the alignment of the second sequence on the first sequence.
for this, I want to have a single alignment line to change the line entirely on the first sequence.
do you have another solution?
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Old 11-08-2015, 03:58 AM   #10
mido1951
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I used Blast to align reads with contigs.
in the final report I have an alignments Strand (Plus / Plus) and Strand (Plus / Minus).
"Minus" is the reverse complement or reverse of my contig?
I know Bastn aligns both ways but do I have to consider the Strand (Plus / Minus)?

I want to identify the parts of alignments contigs with my reads.

thanks for your answer
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