Hello All,

I set up BLAST Search program to making auto typing program.

I have one question "How to bring original sequences" from output file.

For example,

/shared/MiSeq/BLAST/ncbi-blast-2.2.29+/bin/blastn -num_alignments 500 -word_size 50 -db ./test -query ./test.fasta -out ./test.out -outfmt 5

I got output file format as "XML" because of outfmt 5.

I convert this results and programming handling this data.

But I wonder is there any way to get "Original Sequence" in the output format? Or, is there any idea how to handle below cases?

I have one raw sequences like below,

AAAAACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCAAAAA

that "TTTTTTTTTTTTT" positions are Exon2.

So I have a reference like below,

GTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTG

So If I aligned this two It will be like below

-----GTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTG-----
      ||||||||||||||||||||||||||||||||
AAAAACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCAAAAA

BLAST Search results will be 100% match like below,

TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
||||||||||||||||||||||||||||||||
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT

In this case I want to determine whether this raw sequences amplified 100% of that database segment.

This case even though there are 2 mismatch bases are trimmed It is actually fully amplified Exon2.

but Some cases like below does not 100% amplified.

 TTTTTTTTTTTTTTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
 TTTTTTTTTTTTTT---------------------------------------------------------

So below examples are

  Intron 1                          Exon2                 Intron 2
TTTTTTTTTTTTTTTTTTTTTTTTTTT AAAAAAAAAAAAAAAAAAAAAAAAAA TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
                      TTTTT AAAAAAAAAAAAAAAAAAAAAAAAAA TTTTT

It is only Exon2 is fully amplified. I'd like to get this fully amplified sequences (Which segments are fully amplified)

I am thinking to get it from comparing original sequences. Does anyone has good idea? Thank you,