From gilal at md.huji.ac.il Wed Nov 5 09:55:28 2003 From: gilal at md.huji.ac.il (Gila Lithwick) Date: Wed, 05 Nov 2003 16:55:28 +0200 Subject: palindrome Message-ID: <3FA90F60.8070300@md.huji.ac.il> Hello, I ran the emboss program "palindrome" on the sequence K01964. This sequence has an inverted repeat of length 11, occurring at 122-132 and 4672-4682. These inverted repeats have a mismatch at the first base (the entire 11 bases are defined as inverted repeats for several reasons). I noticed two problems when I ran palindrome on this sequence: 1)The "maximum length of palindrome" is actually the maximum length +1. (To search for a specific palindrome length the maximum length must be the minimum length +1). 2) When searching for a repeat of length 11 with at least one mismatch in the above example, the true inverted repeats are not found. I imagine that this is because the mismatch is on the edge, however there is meaning for this type of hit. Thank you, Gila. From fehertrans at interware.hu Sun Nov 16 00:17:30 2003 From: fehertrans at interware.hu (Feher Trans Bt.) Date: Sun, 16 Nov 2003 07:17:30 +0200 Subject: Dear Partner! Message-ID: <20031116060106.A5F4F7D32B@mercury.hgmp.mrc.ac.uk> Dear Partner! Please apologize us for not contacting you for a long time. We recently performed a major structural transformation at the end of which we are on the Internet too. We consider that our present system is more efficient, because the employer can contact directly the applicant, all the information (resume, diplomas, passport copy, criminal and medical records, driving license copy) are online at his disposal, thus the administration is not slowing down the hiring process. Our website is available in six languages in order to ease up the collaboration. Please visit our website at: http://www.job-trans.info. Clicking on the flags on the header, you can choose the appropriate language. If you have any additional questions, please contact us, we are at your service. If there are major changes regarding your labor force request, since our last mail exchange, please send us an updated info, or contact directly the applicants from our database. In the hope of a future collaboration, Regards, Beatrix De Villa FEHER TRANS Ny?ry P?l u. 9/1 1056 Budapest Hungary Tel/Fax: +36 1 317 72 74 e-mail: fehertrans at interware.hu web: http://www.job-trans.info Ps: We apologize for any grammatical errors on our website, some parts of the site are still under development. Your ideas, comment are welcomed in the guest book. If you are interested in our advertising possibilities, please contact us at the above e-mail address. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss-dev/attachments/20031116/99fafddb/attachment.html From jison at hgmp.mrc.ac.uk Fri Nov 21 09:01:31 2003 From: jison at hgmp.mrc.ac.uk (Dr J.C. Ison) Date: Fri, 21 Nov 2003 14:01:31 +0000 Subject: Bioinformatics Software Development Course Message-ID: <3FBE1ABB.CC15EF08@hgmp.mrc.ac.uk> Hi Details on a forthcoming FREE programming course for bioinformatics using EMBOSS are below. Apologies for the spam if not interested. Cheers Jon Jon C. Ison, PhD Bioinformatics Applications Group UK MRC Human Genome Mapping Project Resource Centre Hinxton, Cambridge, CB10 1SB, UK E-mail : jison at hgmp.mrc.ac.uk BSDC 2004 Bioinformatics Software Development Course January 13-15, April 20-22, July 28-30, November 2-4 2004 Following from the highly successful BSDC 2003 courses, a new series of courses on 'Bioinformatics Software Development' using EMBOSS will be held in the training room at Hinxton Hall on January 13-15, April 20-22, July 28-30, November 2-4 2004 The course will give a good introduction to programming in EMBOSS. By the end of the course you will be experienced in all the steps in writing a basic bioinformatics application using the EMBOSS programming libraries. The course would suit competent programmers, probably with at least a couple of years of experience. A reasonable working knowledge of C is required, familiarity with pointers is helpful but not essential. The three dates are likely to get booked up very quickly so please email Karen Hampson (khampson at hgmp.mrc.ac.uk) to register as soon as possible. To read more about the course see http://www.hgmp.mrc.ac.uk/CCP11/CCP11courses/EMBOSS-Course/emboss_index.html To read more about EMBOSS see EMBOSS : http://www.hgmp.mrc.ac.uk/Software/EMBOSS/ From ableasby at hgmp.mrc.ac.uk Sun Nov 30 13:05:49 2003 From: ableasby at hgmp.mrc.ac.uk (Alan Bleasby) Date: Sun, 30 Nov 2003 18:05:49 GMT Subject: EMBOSS coding style Message-ID: <200311301805.hAUI5nVu014368@bromine.hgmp.mrc.ac.uk> Dear developers, Users of CVS may have noticed that a few months ago the whole source tree was changed to reflect coding standards agreed by the core development team. Those changes, of course, are also in the 2.8.0 release just announced. Apart from the obvious advantage that programmers, having become used to the new format, will be able to read each other's code it also enables us to write consistent documentation using code snippets. We'd therefore appreciate it if new submissions to emboss-submit stick to the new format. For emacs users the file: ftp://ftp.uk.embnet.org/pub/EMBOSS/.gnu/.emacs may be a help. The file 'c-mode.el' is in the same directory for those systems lacking the file (put it in your site-lisp directory if so). Thanks in advance and keep them coming. Alan From gilal at md.huji.ac.il Wed Nov 5 14:55:28 2003 From: gilal at md.huji.ac.il (Gila Lithwick) Date: Wed, 05 Nov 2003 16:55:28 +0200 Subject: palindrome Message-ID: <3FA90F60.8070300@md.huji.ac.il> Hello, I ran the emboss program "palindrome" on the sequence K01964. This sequence has an inverted repeat of length 11, occurring at 122-132 and 4672-4682. These inverted repeats have a mismatch at the first base (the entire 11 bases are defined as inverted repeats for several reasons). I noticed two problems when I ran palindrome on this sequence: 1)The "maximum length of palindrome" is actually the maximum length +1. (To search for a specific palindrome length the maximum length must be the minimum length +1). 2) When searching for a repeat of length 11 with at least one mismatch in the above example, the true inverted repeats are not found. I imagine that this is because the mismatch is on the edge, however there is meaning for this type of hit. Thank you, Gila. From fehertrans at interware.hu Sun Nov 16 05:17:30 2003 From: fehertrans at interware.hu (Feher Trans Bt.) Date: Sun, 16 Nov 2003 07:17:30 +0200 Subject: Dear Partner! Message-ID: <20031116060106.A5F4F7D32B@mercury.hgmp.mrc.ac.uk> Dear Partner! Please apologize us for not contacting you for a long time. We recently performed a major structural transformation at the end of which we are on the Internet too. We consider that our present system is more efficient, because the employer can contact directly the applicant, all the information (resume, diplomas, passport copy, criminal and medical records, driving license copy) are online at his disposal, thus the administration is not slowing down the hiring process. Our website is available in six languages in order to ease up the collaboration. Please visit our website at: http://www.job-trans.info. Clicking on the flags on the header, you can choose the appropriate language. If you have any additional questions, please contact us, we are at your service. If there are major changes regarding your labor force request, since our last mail exchange, please send us an updated info, or contact directly the applicants from our database. In the hope of a future collaboration, Regards, Beatrix De Villa FEHER TRANS Ny?ry P?l u. 9/1 1056 Budapest Hungary Tel/Fax: +36 1 317 72 74 e-mail: fehertrans at interware.hu web: http://www.job-trans.info Ps: We apologize for any grammatical errors on our website, some parts of the site are still under development. Your ideas, comment are welcomed in the guest book. If you are interested in our advertising possibilities, please contact us at the above e-mail address. -------------- next part -------------- An HTML attachment was scrubbed... URL: From jison at hgmp.mrc.ac.uk Fri Nov 21 14:01:31 2003 From: jison at hgmp.mrc.ac.uk (Dr J.C. Ison) Date: Fri, 21 Nov 2003 14:01:31 +0000 Subject: Bioinformatics Software Development Course Message-ID: <3FBE1ABB.CC15EF08@hgmp.mrc.ac.uk> Hi Details on a forthcoming FREE programming course for bioinformatics using EMBOSS are below. Apologies for the spam if not interested. Cheers Jon Jon C. Ison, PhD Bioinformatics Applications Group UK MRC Human Genome Mapping Project Resource Centre Hinxton, Cambridge, CB10 1SB, UK E-mail : jison at hgmp.mrc.ac.uk BSDC 2004 Bioinformatics Software Development Course January 13-15, April 20-22, July 28-30, November 2-4 2004 Following from the highly successful BSDC 2003 courses, a new series of courses on 'Bioinformatics Software Development' using EMBOSS will be held in the training room at Hinxton Hall on January 13-15, April 20-22, July 28-30, November 2-4 2004 The course will give a good introduction to programming in EMBOSS. By the end of the course you will be experienced in all the steps in writing a basic bioinformatics application using the EMBOSS programming libraries. The course would suit competent programmers, probably with at least a couple of years of experience. A reasonable working knowledge of C is required, familiarity with pointers is helpful but not essential. The three dates are likely to get booked up very quickly so please email Karen Hampson (khampson at hgmp.mrc.ac.uk) to register as soon as possible. To read more about the course see http://www.hgmp.mrc.ac.uk/CCP11/CCP11courses/EMBOSS-Course/emboss_index.html To read more about EMBOSS see EMBOSS : http://www.hgmp.mrc.ac.uk/Software/EMBOSS/ From ableasby at hgmp.mrc.ac.uk Sun Nov 30 18:05:49 2003 From: ableasby at hgmp.mrc.ac.uk (Alan Bleasby) Date: Sun, 30 Nov 2003 18:05:49 GMT Subject: EMBOSS coding style Message-ID: <200311301805.hAUI5nVu014368@bromine.hgmp.mrc.ac.uk> Dear developers, Users of CVS may have noticed that a few months ago the whole source tree was changed to reflect coding standards agreed by the core development team. Those changes, of course, are also in the 2.8.0 release just announced. Apart from the obvious advantage that programmers, having become used to the new format, will be able to read each other's code it also enables us to write consistent documentation using code snippets. We'd therefore appreciate it if new submissions to emboss-submit stick to the new format. For emacs users the file: ftp://ftp.uk.embnet.org/pub/EMBOSS/.gnu/.emacs may be a help. The file 'c-mode.el' is in the same directory for those systems lacking the file (put it in your site-lisp directory if so). Thanks in advance and keep them coming. Alan