From qas20030409 at qa-systems.com Wed Apr 9 12:17:38 2003 From: qas20030409 at qa-systems.com (QA Systems) Date: Wed, 9 Apr 2003 18:17:38 +0200 Subject: Java Software Quality Problems? Message-ID: <200304091617.h39GHci15736@qarouter.qasystems.com> An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss-dev/attachments/20030409/776206b6/attachment.html From gbottu at ben.vub.ac.be Mon Apr 14 13:07:45 2003 From: gbottu at ben.vub.ac.be (Guy Bottu) Date: Mon, 14 Apr 2003 19:07:45 +0200 (CEST) Subject: Preferred isoschizomer ? Message-ID: <200304141707.h3EH7jV31381945@black.vub.ac.be> from : BEN Dear colleagues, A user of BEN complained about a serious problem with restrict/remap. He could not find the site for PstI in a sequence, where the "wet work" showed the enzyme did cut. He lost a lot of time because he thought he had made an error, while the reason was that the program reported the isoshizomer BspMAI. Now, in the Rebase we see : <1>BspMAI <2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I ,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp9 3I,Bsp107I,Bsp1..... So, PstI is clearly identified as the prototype enzyme. Yet, when restrict is requested to report only the "preferred" isoschizomer, it does not report PstI, nor even the first in the file (AinI) or the last (YenEI). Does someone understand the cause of the erratic behaviour ? And did noone else suffer from this "feature" ? Regards, Guy Bottu From ableasby at hgmp.mrc.ac.uk Mon Apr 14 14:17:54 2003 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Mon, 14 Apr 2003 19:17:54 +0100 (BST) Subject: Preferred isoschizomer ? Message-ID: <200304141817.h3EIHs410930@bromine.hgmp.mrc.ac.uk> 1) If your colleague had explicitly said -enzymes psti on the command line (or equivalent GUI) then it would be found. The output would be overly verbose if all isoschizomers are reported so as a compromise it reports only one. 2) If you take the emboss files from the REBASE (NEB) distro then, after renaming and putting them in data/REBASE, it will probably report PstI (haven't tried it). I arranged with NEB that they would provide only the 'common' REs in their files. I believe this is what some other packages do. Using REBASEEXTRACT on the withrefm file gives all the REs. 3) You can equate any reported RE to another by adding an entry into embossre.equ e.g. BspMAI PstI HTH Alan From gbottu at black.vub.ac.be Tue Apr 15 14:54:31 2003 From: gbottu at black.vub.ac.be (Guy Bottu) Date: Tue, 15 Apr 2003 20:54:31 +0200 Subject: Preferred isischizomer (bis) Message-ID: <20030415205431.A1419113@black.vub.ac.be> from : BEN Dear colleagues, Allow me to insist. The point is that when you ask for only one representative isoschizomer the programs should report PstI, because PstI is mentioned in Rebase as the "prototype". The GCG programs map, mapplot and mapsort did do this. The file in GCG format contains : ;BstMAI 5 C_TGCA'G -4 PstI 5 C_TGCA'G -4 While withrefm contains the same information in another way. So, IMHO, rebaseextract and/or restrict+remap are not doing their job properly. Sincerely, Guy Bottu From gbottu at black.vub.ac.be Thu Apr 24 04:56:15 2003 From: gbottu at black.vub.ac.be (Guy Bottu) Date: Thu, 24 Apr 2003 10:56:15 +0200 Subject: Preferred isoschizomer (bis) In-Reply-To: <003d01c30a31$4813ac70$0402a6c1@windows.csc.fi>; from eija.korpelainen@csc.fi on Thu, Apr 24, 2003 at 10:15:27AM +0300 References: <20030415205431.A1419113@black.vub.ac.be> <003d01c30a31$4813ac70$0402a6c1@windows.csc.fi> Message-ID: <20030424105615.A1078815@black.vub.ac.be> Dear colleagues, I took a second look, and it is even worse : the file withrefm.304 contains as many as 149 enzymes with restriction site CTGCAG. The file embossre.enz contains 2 sites CTGCAG (BspMAI and PstI) and 147 sites ctgcag. When I run restrict with parameter -nolimit it finds the 2 sites and when I run it in default mode it finds only BspMAI. There is clearly a bug+misfeature in the programs rebaseextract+restrict. One would expect that restrict by default finds PstI and with -nolimit finds all 149 enzymes (although this would give a monstrous output). Sincerely, Guy Bottu From qas20030409 at qa-systems.com Wed Apr 9 16:17:38 2003 From: qas20030409 at qa-systems.com (QA Systems) Date: Wed, 9 Apr 2003 18:17:38 +0200 Subject: Java Software Quality Problems? Message-ID: <200304091617.h39GHci15736@qarouter.qasystems.com> An HTML attachment was scrubbed... URL: From gbottu at ben.vub.ac.be Mon Apr 14 17:07:45 2003 From: gbottu at ben.vub.ac.be (Guy Bottu) Date: Mon, 14 Apr 2003 19:07:45 +0200 (CEST) Subject: Preferred isoschizomer ? Message-ID: <200304141707.h3EH7jV31381945@black.vub.ac.be> from : BEN Dear colleagues, A user of BEN complained about a serious problem with restrict/remap. He could not find the site for PstI in a sequence, where the "wet work" showed the enzyme did cut. He lost a lot of time because he thought he had made an error, while the reason was that the program reported the isoshizomer BspMAI. Now, in the Rebase we see : <1>BspMAI <2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I ,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp9 3I,Bsp107I,Bsp1..... So, PstI is clearly identified as the prototype enzyme. Yet, when restrict is requested to report only the "preferred" isoschizomer, it does not report PstI, nor even the first in the file (AinI) or the last (YenEI). Does someone understand the cause of the erratic behaviour ? And did noone else suffer from this "feature" ? Regards, Guy Bottu From ableasby at hgmp.mrc.ac.uk Mon Apr 14 18:17:54 2003 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Mon, 14 Apr 2003 19:17:54 +0100 (BST) Subject: Preferred isoschizomer ? Message-ID: <200304141817.h3EIHs410930@bromine.hgmp.mrc.ac.uk> 1) If your colleague had explicitly said -enzymes psti on the command line (or equivalent GUI) then it would be found. The output would be overly verbose if all isoschizomers are reported so as a compromise it reports only one. 2) If you take the emboss files from the REBASE (NEB) distro then, after renaming and putting them in data/REBASE, it will probably report PstI (haven't tried it). I arranged with NEB that they would provide only the 'common' REs in their files. I believe this is what some other packages do. Using REBASEEXTRACT on the withrefm file gives all the REs. 3) You can equate any reported RE to another by adding an entry into embossre.equ e.g. BspMAI PstI HTH Alan From gbottu at black.vub.ac.be Tue Apr 15 18:54:31 2003 From: gbottu at black.vub.ac.be (Guy Bottu) Date: Tue, 15 Apr 2003 20:54:31 +0200 Subject: Preferred isischizomer (bis) Message-ID: <20030415205431.A1419113@black.vub.ac.be> from : BEN Dear colleagues, Allow me to insist. The point is that when you ask for only one representative isoschizomer the programs should report PstI, because PstI is mentioned in Rebase as the "prototype". The GCG programs map, mapplot and mapsort did do this. The file in GCG format contains : ;BstMAI 5 C_TGCA'G -4 PstI 5 C_TGCA'G -4 While withrefm contains the same information in another way. So, IMHO, rebaseextract and/or restrict+remap are not doing their job properly. Sincerely, Guy Bottu From gbottu at black.vub.ac.be Thu Apr 24 08:56:15 2003 From: gbottu at black.vub.ac.be (Guy Bottu) Date: Thu, 24 Apr 2003 10:56:15 +0200 Subject: Preferred isoschizomer (bis) In-Reply-To: <003d01c30a31$4813ac70$0402a6c1@windows.csc.fi>; from eija.korpelainen@csc.fi on Thu, Apr 24, 2003 at 10:15:27AM +0300 References: <20030415205431.A1419113@black.vub.ac.be> <003d01c30a31$4813ac70$0402a6c1@windows.csc.fi> Message-ID: <20030424105615.A1078815@black.vub.ac.be> Dear colleagues, I took a second look, and it is even worse : the file withrefm.304 contains as many as 149 enzymes with restriction site CTGCAG. The file embossre.enz contains 2 sites CTGCAG (BspMAI and PstI) and 147 sites ctgcag. When I run restrict with parameter -nolimit it finds the 2 sites and when I run it in default mode it finds only BspMAI. There is clearly a bug+misfeature in the programs rebaseextract+restrict. One would expect that restrict by default finds PstI and with -nolimit finds all 149 enzymes (although this would give a monstrous output). Sincerely, Guy Bottu