[emboss-dev] Enquiry about emboss needle program customizin​g

[Tae-Kyung Kim]

*I am now working for Korea Bioinformation Center, and particularly
integrating Korean Bio-resources as National infrastructure.*
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*Now, I am urgently customizing global alignment program needle *
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*for fungi sequence database analysis. Although I know that emboss needle is
the best program, *
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*it is not easy to customize it for my purpose. Would you please let me know
how to modify the program?*
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*There are two questions.*
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*First, I would like to get standard input sequence parameter instead of
file name like this.*
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*./needle -asequence ATGCATATAAA -bsequence ATAGAATAAA -gapopen 10
-gapextend 0.5 -stdout -auto*
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*I want to reduce file I/O to perform large number of global sequence
alignment with this structure.*
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*Second, I would like to get real identity, which means the number of '|' in
needle result.*
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*                  ATAAAAAA*
*                   | | | |    | | |                    *
*                  ATAATAAA*
*    ---------------------------------------*
*              Real Identity = 7*
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*I thank you in advance for your support and look forward to hearing from
you.*

-- 
Tae-Kyung Kim, Ph.D.
Bio-Resource Information Team
Korea Bioinformation Center (KOBIC)
111 Gwahangno, Yuseong-gu, Daejeon 305-806, Korea
TEL: +82-42-879-8548
FAX: +82-42-879-8519