Description:
The Staden molecular sequence analysis software. (Moderated)
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Biomedical and Bioinformatics Conference - Call for Papers
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Appologies for multiple receptions ------------------------------ ------ Thank you for circulating this announcement ------------------------------ -------------- Call for Papers - International Conference on Advances in Biomedical engineering (C2B 2011) - Lebanese University, Azm Center for Biotechnology... more »
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SAMtools?
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Hi I am attempting to install Staden on a 64 bit Ubuntu 10.04 linux box with Phre/Phrap/Consed already installed. The error I continue to get on install is with the lack of SAMtools. Where can I get this, is there a specific version I need for Staden, how do I install it? Does anyone have any updates on installation of the new version of Staden on Ubuntu?... more »
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problem in heterozygous indels
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Hi, I use staden for DNA sequence assembly and I use staden in windows. the sequence on which i am working now is heterozygous and it has INDELs in it. the software shows the presence of INDELs but it do not give two separate sequences. Can you please help me in solving this problem Regards, Abdul... more »
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Error codes
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Hello !!! Please I would like to know about the meaning of some pregap4's error codes. In file pregap.log the information about the failed files (here just two) is: home/... /10f.exp (EXP) ERROR: screen_vector: 11r.exp (???) ERROR: gap4_assemble: failed with code 1 basically I use the same setup with many files and just few has error... more »
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How to install Staden 1.7.0 on Mac OS 10.5?
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Hi, I have a stupid question. I'm trying to install Staden 1.7.0 on Mac OS 10.5. After I unzip the file that I downloaded from Softpedia ([link] Download-27956.html), I can't figure out how to install it. Can anyone tell me tell me how to do it? Thanks!... more »
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gap4 running problem load_alignment_matrix error
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Hi, I am trying to install Staden Gap4 on a 64 bit machine with Ubuntu installed. It appears that trev & pregap will start. But when I type gap4& I get this message - invalid command name "load_alignment_matrix" while executing "load_alignment_matrix [keylget gap_defs ALIGNMENT.MATRIX_FILE]"... more »
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phred and pregap4
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Hello, I apologise in advance if this is a stupid question. I couldn't seem to find this in the staden help documentation. Where do I install phred so that it can be accessed by the pregap4 phred module. Thank you, Glenn
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invalid command name "open_db"
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Hello, staden-linux-1-6-0 here. It seems that 'open_db' is missing from this release?! I tried "find $STADENROOT -name open_db" to no avail ... (and yes, $STADENROOT is set correctly). I was going through $STADENROOT/course/ unix_docs/course_unix.pdf, and I got as far as page 30 (36), when gap4 failed with the error:... more »
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permission for publication
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Dear Staden developers, I would like to know if I need any special permission from you you to publish a screenshot created by your software Trev (trace viewer)? If yes, please let me know what should I do to get it. Thank you, Alla L.Lapidus, Ph.D DOE_JGI
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