From dgarboczi at niaid.nih.gov Wed Jan 9 15:18:27 2008 From: dgarboczi at niaid.nih.gov (David Garboczi) Date: Wed Jan 9 15:18:35 2008 Subject: [Jalview-discuss] numbering Message-ID: I would like the numbering across the top of the alignment to start at other than 1. I'd like the first residue of the top sequence to be 6, for instance. How to do it? 2nd question, I would like the numbering to follow the number of residues of the top sequence. not assigning numbers to gaps. Or are these items I should change in Illustrator? Mac OS 10.4.11, Firefox, latest java thanks, Dave -- David N. Garboczi, PhD Phone: 301-496-4773 Investigator, Structural Biology Section (SBS) Laboratory of Immunogenetics (LIG) National Institute of Allergy and Infectious Diseases (NIAID) National Institutes of Health (NIH) Twinbrook 2/Room 110 12441 Parklawn Drive Rockville, Maryland 20852-1742 Fax: 301-402-0284 Email: dgarboczi@niaid.nih.gov The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. The National Institute of Allergy and Infectious Diseases (NIAID) shall not accept liability for any statement made that are the sender's own and not expressly made on behalf of the NIAID by one of its representatives. From dgarboczi at niaid.nih.gov Wed Jan 9 15:40:08 2008 From: dgarboczi at niaid.nih.gov (David Garboczi) Date: Wed Jan 9 15:40:19 2008 Subject: [Jalview-discuss] need more space between right-justified names and the sequences Message-ID: If I right-justify the sequence names, they are too close to the sequence. When I try to move the sequences to the right, the names move too. If the sequence names are not right-justified, then I can move the sequences to the right to make more space between the name and the sequence. Dave -- David N. Garboczi, PhD Phone: 301-496-4773 Investigator, Structural Biology Section (SBS) Laboratory of Immunogenetics (LIG) National Institute of Allergy and Infectious Diseases (NIAID) National Institutes of Health (NIH) Twinbrook 2/Room 110 12441 Parklawn Drive Rockville, Maryland 20852-1742 Fax: 301-402-0284 Email: dgarboczi@niaid.nih.gov The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. The National Institute of Allergy and Infectious Diseases (NIAID) shall not accept liability for any statement made that are the sender's own and not expressly made on behalf of the NIAID by one of its representatives. From jimp at compbio.dundee.ac.uk Sat Jan 12 20:23:42 2008 From: jimp at compbio.dundee.ac.uk (Jim Procter) Date: Sat Jan 12 20:24:03 2008 Subject: [Jalview-discuss] numbering In-Reply-To: References: Message-ID: <478921CE.3070207@compbio.dundee.ac.uk> Hi Dave. David Garboczi wrote: > I would like the numbering across the top of the alignment to start at > other than 1. I'd like the first residue of the top sequence to be 6, > for instance. > How to do it? > > 2nd question, I would like the numbering to follow the number of > residues of the top sequence. not assigning numbers to gaps. These questions sound like much the same thing. Basically, you'd like to be able to pick what coordinate system is used for the alignment ruler - alignment columns, or the positions w.r.t.one of the aligned sequences. > > Or are these items I should change in Illustrator? for the moment, yes. I can see that this would be a very useful thing to be able to do - but there isn't any way to do this in Jalview as it stands. I also know how much of a pain it will be making these changes by hand in illustrator. sorry. Jim. From jimp at compbio.dundee.ac.uk Sat Jan 12 20:32:37 2008 From: jimp at compbio.dundee.ac.uk (Jim Procter) Date: Sat Jan 12 20:32:42 2008 Subject: [Jalview-discuss] need more space between right-justified names and the sequences In-Reply-To: References: Message-ID: <478923E5.2050708@compbio.dundee.ac.uk> Hi again, Dave. David Garboczi wrote: > If I right-justify the sequence names, they are too close to the > sequence. When I try to move the sequences to the right, the names > move too. > > If the sequence names are not right-justified, then I can move the > sequences to the right to make more space between the name and the > sequence. The sequence label area width can be adjusted - and of course, when the sequences are right justified, they are placed relative to the right hand border of the label area, so increasing the width of the sequence label area moves the labels to the right. It sounds like you want to add a right-hand margin that can be adjusted independently of the width of the label area. The quickest way to deal with this is to use illustrator (or something else!) to move the labels to the left. We could add a label area margin into Jalview, but there are more pressing layout issues to be fixed first. The ones that come to mind are automatically adjusting the width of the label area, or allowing it to be scrolled to the left or right independently of the alignment. thanks for posting these comments and feature requests.. Jim -- ------------------------------------------------------------------- J. B. Procter (VAMSAS Project) Barton Bioinformatics Research Group Phone/Fax:+44(0)1382 388734/345764 http://www.compbio.dundee.ac.uk From geoff at compbio.dundee.ac.uk Mon Jan 14 08:16:52 2008 From: geoff at compbio.dundee.ac.uk (Geoff Barton) Date: Mon Jan 14 08:15:38 2008 Subject: [Jalview-discuss] numbering In-Reply-To: <478921CE.3070207@compbio.dundee.ac.uk> References: <478921CE.3070207@compbio.dundee.ac.uk> Message-ID: Although you can't do this in Jalview, you can do it in ALSCRIPT. However, ALSCRIPT takes a lot more learning than Jalview - it is a command-driven program rather than graphical point-and-click. It may be easier for a one-off alignment just to modify a .ps file in Illustrator. Geoff. On Sat, 12 Jan 2008, Jim Procter wrote: > Hi Dave. > > David Garboczi wrote: >> I would like the numbering across the top of the alignment to start at >> other than 1. I'd like the first residue of the top sequence to be 6, for >> instance. >> How to do it? >> >> 2nd question, I would like the numbering to follow the number of residues >> of the top sequence. not assigning numbers to gaps. > These questions sound like much the same thing. Basically, you'd like to be > able to pick what coordinate system is used for the alignment ruler - > alignment columns, or the positions w.r.t.one of the aligned sequences. >> >> Or are these items I should change in Illustrator? > for the moment, yes. I can see that this would be a very useful thing to be > able to do - but there isn't any way to do this in Jalview as it stands. I > also know how much of a pain it will be making these changes by hand in > illustrator. > > sorry. > Jim. > > _______________________________________________ > Jalview-discuss mailing list > Jalview-discuss@jalview.org > http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss > -- Geoff Barton, Professor of Bioinformatics, School of Life Sciences University of Dundee, Scotland, UK. geoff@compbio.dundee.ac.uk Tel:+44 1382 385860/388731 (Fax:385764) www.compbio.dundee.ac.uk From JLR at ssi.dk Mon Jan 28 10:49:26 2008 From: JLR at ssi.dk (Jonas Larsson) Date: Mon Jan 28 10:49:51 2008 Subject: [Jalview-discuss] Find in nucleotide files? Message-ID: <479DC146.B062.0032.0@ssi.dk> Why is it that I can not search on sequences if they are nucleotides? If I am working on amino acid sequences everything works OK but with nucleotides it seems impossible. Have anyone else had this problem as well? I simply get no results or a "0 matches found" found every time. / Jonas -- STATENS SERUM INSTITUT - 5, Artillerivej - DK-2300 Copenhagen S Tel: +45 3268 3268 - Fax: +45 3268 3868 serum@ssi.dk www.ssi.dk This e-mail, inclusive of attachments, is intended for the person(s) or entity stated above and may contain confidential information. Unauthorised reading, disclosure, copying, distribution or use of this information may violate rights to proprietary information. If you are not an intended recipient, please return this e-mail to the sender and delete your copy. Thank you. From jimp at compbio.dundee.ac.uk Mon Jan 28 17:16:17 2008 From: jimp at compbio.dundee.ac.uk (James Procter) Date: Mon Jan 28 17:16:35 2008 Subject: [Jalview-discuss] Find in nucleotide files? In-Reply-To: <479DC146.B062.0032.0@ssi.dk> References: <479DC146.B062.0032.0@ssi.dk> Message-ID: <479E0DE1.80405@compbio.dundee.ac.uk> Jonas Larsson wrote: > Why is it that I can not search on sequences if they are nucleotides? If I am working on amino acid sequences everything works OK but with nucleotides it seems impossible. Have anyone else had this problem as well? I simply get no results or a "0 matches found" found every time. what version are you using, Jonas ? It seems to work fine with the current version available from the website. The find function tries to be slightly intelligent so it might be matching on sequence ID, sequence position or sequence string (excluding gaps and optionally matching case). Can you show it doesn't work for a really simple case ? Jim From JLR at ssi.dk Tue Jan 29 07:39:15 2008 From: JLR at ssi.dk (Jonas Larsson) Date: Tue Jan 29 07:39:33 2008 Subject: [Jalview-discuss] Find in nucleotide files? In-Reply-To: <479E0DE1.80405@compbio.dundee.ac.uk> References: <479DC146.B062.0032.0@ssi.dk> <479E0DE1.80405@compbio.dundee.ac.uk> Message-ID: <479EE632.B062.0032.0@ssi.dk> >>> On 28-01-2008 at 18:16, James Procter wrote: > Jonas Larsson wrote: >> Why is it that I can not search on sequences if they are nucleotides? If I > am working on amino acid sequences everything works OK but with nucleotides > it seems impossible. Have anyone else had this problem as well? I simply get > no results or a "0 matches found" found every time. > what version are you using, Jonas ? 2.3 May 24, I also tried with the Web start version directly from the web page (2.3 May 10). Same behaviour in both. Java 1.6.0_03-b05 > It seems to work fine with the current version available from the > website. The find function tries to be slightly intelligent so it might > be matching on sequence ID, sequence position or sequence string > (excluding gaps and optionally matching case). Can you show it doesn't > work for a really simple case ? This is as simple as it gets. http://www.e-tintin.com/test_find.png In the top part trying to find in the nucleotide sequence and in the bottom one in the protein one. For simplicity sake I used the find all, but the result is the same regardless of that. / Jonas -- Jonas Larsson, M.Sc. Ph.D. Bacterial Typing Department of Bacteriology, Mycology & Parasitology Statens Serum Institut Bygning 37b, 133 Artillerivej 5 2300 Copenhagen S Denmark Phone: (+45) 3268 3221 Fax: (+45) 3268 3868 STATENS SERUM INSTITUT - 5, Artillerivej - DK-2300 Copenhagen S Tel: +45 3268 3268 - Fax: +45 3268 3868 serum@ssi.dk www.ssi.dk This e-mail, inclusive of attachments, is intended for the person(s) or entity stated above and may contain confidential information. Unauthorised reading, disclosure, copying, distribution or use of this information may violate rights to proprietary information. If you are not an intended recipient, please return this e-mail to the sender and delete your copy. Thank you. From jimp at compbio.dundee.ac.uk Tue Jan 29 09:11:45 2008 From: jimp at compbio.dundee.ac.uk (James Procter) Date: Tue Jan 29 09:11:56 2008 Subject: [Jalview-discuss] Find in nucleotide files? In-Reply-To: <479EE632.B062.0032.0@ssi.dk> References: <479DC146.B062.0032.0@ssi.dk> <479E0DE1.80405@compbio.dundee.ac.uk> <479EE632.B062.0032.0@ssi.dk> Message-ID: <479EEDD1.6000200@compbio.dundee.ac.uk> Thanks for putting up the example image, Jonas. You've found a bug in the Find function. It won't find anything when doing a case-insensitive search in lower-case sequences, which is kind of annoying... to say the least, and not just restricted to dna. The workaround for the moment is to check the 'case sensitive' box when you search dna, and make sure that both the query and the dna is in lower case - or alternatively uppercase all the dna (see the edit submenu of the pop-up menu). It'll be fixed in the development version in about half an hour... Jim -- ------------------------------------------------------------------- J. B. Procter (VAMSAS Project) Barton Bioinformatics Research Group Phone/Fax:+44(0)1382 388734/345764 http://www.compbio.dundee.ac.uk From jimp at compbio.dundee.ac.uk Tue Jan 29 09:28:21 2008 From: jimp at compbio.dundee.ac.uk (James Procter) Date: Tue Jan 29 09:28:32 2008 Subject: [Jalview-discuss] Jalview Development Version. Message-ID: <479EF1B5.4060104@compbio.dundee.ac.uk> Hello all. I just realised that whilst mentioning the Jalview development version in the last message (to Jonas), I haven't actually said where it is. There is a publicly available automated development build which is updated every time the Jalview CVS is updated. In addition to the normal disclaimers that accompany GPL software, please remember that this version comes with even less than zero guarantee of being stable or reliable. That said, you can get it here : http://www.compbio.dundee.ac.uk/~ws-dev1/jalview/latest/webstart/jalview.jnlp We are gearing up for the release of Jalview 2.4, so any feedback would be gratefully received. If you run across any glaring bugs in the automated build above, please tell us about it here or (preferably) on the help@jalview.org address. Cheers. Jim. -- ------------------------------------------------------------------- J. B. Procter (VAMSAS/ENFIN) Barton Bioinformatics Research Group Phone/Fax:+44(0)1382 388734/345764 http://www.compbio.dundee.ac.uk From JLR at ssi.dk Tue Jan 29 12:51:16 2008 From: JLR at ssi.dk (Jonas Larsson) Date: Tue Jan 29 12:51:42 2008 Subject: [Jalview-discuss] Find in nucleotide files? In-Reply-To: <479EEDD1.6000200@compbio.dundee.ac.uk> References: <479DC146.B062.0032.0@ssi.dk> <479E0DE1.80405@compbio.dundee.ac.uk> <479EE632.B062.0032.0@ssi.dk> <479EEDD1.6000200@compbio.dundee.ac.uk> Message-ID: <479F2F54.B062.0032.0@ssi.dk> >>> On 29-01-2008 at 10:11, James Procter wrote: > Thanks for putting up the example image, Jonas. > > You've found a bug in the Find function. It won't find anything when > doing a case-insensitive search in lower-case sequences, which is kind > of annoying... to say the least, and not just restricted to dna. The > workaround for the moment is to check the 'case sensitive' box when you > search dna, and make sure that both the query and the dna is in lower > case - or alternatively uppercase all the dna (see the edit submenu of > the pop-up menu). Ah! Excellent! Now the find works everywhere :) Quick fix on the development version as well! Thanks a lot. / jonas STATENS SERUM INSTITUT - 5, Artillerivej - DK-2300 Copenhagen S Tel: +45 3268 3268 - Fax: +45 3268 3868 serum@ssi.dk www.ssi.dk This e-mail, inclusive of attachments, is intended for the person(s) or entity stated above and may contain confidential information. Unauthorised reading, disclosure, copying, distribution or use of this information may violate rights to proprietary information. If you are not an intended recipient, please return this e-mail to the sender and delete your copy. Thank you. From JLR at ssi.dk Tue Jan 29 13:06:35 2008 From: JLR at ssi.dk (Jonas Larsson) Date: Tue Jan 29 13:06:55 2008 Subject: [Jalview-discuss] Copy raw sequence! Message-ID: <479F32EA.B062.0032.0@ssi.dk> Hi again jalviewers. I have one wish for the next version that would make a _huge_ difference for the way at least I am using Jalview. That would be an option to use copy the sequence raw instead of as fasta. The reason is that while analysing alignments I wish to check parts of the sequence in a host of other tools and sometimes fasta format is good, more oftenthe applications puke on it. For my part the best thing would be to use ctrl-c for raw copy and ctrl-shift-c for fasta copy. This is of course not a good idea as a default for jalview since that would not be backwards compatible but one could always wish for two additions: raw copy on ctrl-shift-c as default and a checkbox in preferences to swap the two copy variants... As of now I am actually using MEGA in parallel with jalview just for this reason, quite inefficient but stripping out fasta headers all time was even worse :( / Jonas STATENS SERUM INSTITUT - 5, Artillerivej - DK-2300 Copenhagen S Tel: +45 3268 3268 - Fax: +45 3268 3868 serum@ssi.dk www.ssi.dk This e-mail, inclusive of attachments, is intended for the person(s) or entity stated above and may contain confidential information. Unauthorised reading, disclosure, copying, distribution or use of this information may violate rights to proprietary information. If you are not an intended recipient, please return this e-mail to the sender and delete your copy. Thank you. From JLR at ssi.dk Tue Jan 29 13:24:32 2008 From: JLR at ssi.dk (Jonas Larsson) Date: Tue Jan 29 13:24:53 2008 Subject: [Jalview-discuss] IUPAC search in nucleotide sequences Message-ID: <479F371F.B062.0032.0@ssi.dk> Ok, so one more thing while I am at it. Searching with regexes is fine and powerful with protein sequences but when dealing with nucleotide sequences the IUPAC codes are the only reasonable way to go in my opinion. Would it be possible to have IUPAC as a checkbox in the find dialogue? As far as I can see, jalview does not know whether it is analysing nucleotides or aa so automating this would be a larger undertaking, but a checkbox which remembers its state would be just excellent :) Ok, enough for now... STATENS SERUM INSTITUT - 5, Artillerivej - DK-2300 Copenhagen S Tel: +45 3268 3268 - Fax: +45 3268 3868 serum@ssi.dk www.ssi.dk This e-mail, inclusive of attachments, is intended for the person(s) or entity stated above and may contain confidential information. Unauthorised reading, disclosure, copying, distribution or use of this information may violate rights to proprietary information. If you are not an intended recipient, please return this e-mail to the sender and delete your copy. Thank you. From jimp at compbio.dundee.ac.uk Tue Jan 29 14:19:55 2008 From: jimp at compbio.dundee.ac.uk (James Procter) Date: Tue Jan 29 14:20:06 2008 Subject: [Jalview-discuss] Copy raw sequence! In-Reply-To: <479F32EA.B062.0032.0@ssi.dk> References: <479F32EA.B062.0032.0@ssi.dk> Message-ID: <479F360B.2070906@compbio.dundee.ac.uk> Jonas Larsson wrote: > Hi again jalviewers. I have one wish for the next version that would make a _huge_ difference for the way at least I am using Jalview. That would be an option to use copy the sequence raw instead of as fasta. The reason is that while analysing alignments I wish to check parts of the sequence in a host of other tools and sometimes fasta format is good, more oftenthe applications puke on it. > > For my part the best thing would be to use ctrl-c for raw copy and ctrl-shift-c for fasta copy. This is of course not a good idea as a default for jalview since that would not be backwards compatible but one could always wish for two additions: raw copy on ctrl-shift-c as default and a checkbox in preferences to swap the two copy variants... > > As of now I am actually using MEGA in parallel with jalview just for this reason, quite inefficient but stripping out fasta headers all time was even worse :( I'd vote for having a preference (or something) for what jalview uses to copy the data to the clipboard. The application doesn't even touch the clipboard when copies occur internally so internal compatibility for the CTRL-C behaviour isn't really an issue. From what you said about using MEGA, it sounds like you might be interested in TOPALi (http://www.topali.org) which is developed by one of our colaborators. We've implemented an experimental mechanism (the Vamsas menu in either the jalview desktop or the topali main window) for data exchange between the applications for dealing with exactly the kind of situation your are in - moving data between programs to do combined analysis. thanks for the good idea... Jim From jimp at compbio.dundee.ac.uk Tue Jan 29 14:20:03 2008 From: jimp at compbio.dundee.ac.uk (James Procter) Date: Tue Jan 29 14:20:25 2008 Subject: [Jalview-discuss] IUPAC search in nucleotide sequences In-Reply-To: <479F371F.B062.0032.0@ssi.dk> References: <479F371F.B062.0032.0@ssi.dk> Message-ID: <479F3613.9060807@compbio.dundee.ac.uk> Jonas Larsson wrote: > Ok, so one more thing while I am at it. Searching with regexes is fine and powerful with protein sequences but when dealing with nucleotide sequences the IUPAC codes are the only reasonable way to go in my opinion. Would it be possible to have IUPAC as a checkbox in the find dialogue? As far as I can see, jalview does not know whether it is analysing nucleotides or aa so automating this would be a larger undertaking, but a checkbox which remembers its state would be just excellent :) All possible in principle, and it would certainly be useful for those who don't live and breath regex. We'll see what the next Jalview post-doc says when they take up their position. > > Ok, enough for now... cheers :) Jim From JLR at ssi.dk Thu Jan 31 09:21:48 2008 From: JLR at ssi.dk (Jonas Larsson) Date: Thu Jan 31 09:22:10 2008 Subject: [Jalview-discuss] IUPAC search in nucleotide sequences In-Reply-To: <479F3613.9060807@compbio.dundee.ac.uk> References: <479F371F.B062.0032.0@ssi.dk> <479F3613.9060807@compbio.dundee.ac.uk> Message-ID: <47A1A13C.B062.0032.0@ssi.dk> >>> On 29-01-2008 at 15:20, James Procter wrote: > Jonas Larsson wrote: >> Ok, so one more thing while I am at it. Searching with regexes is fine and >> powerful with protein sequences but when dealing with nucleotide sequences >> the IUPAC codes are the only reasonable way to go in my opinion. Would it be >> possible to have IUPAC as a checkbox in the find dialogue? As far as I can >> see, jalview does not know whether it is analysing nucleotides or aa so >> automating this would be a larger undertaking, but a checkbox which remembers >> its state would be just excellent :) > All possible in principle, and it would certainly be useful for those > who don't live and breath regex. We'll see what the next Jalview > post-doc says when they take up their position. Regexes are excellent in many situations, but as it is; many other software uses the iupac one-letter code and cutting and pasting sequences gets cumbersome. In the meantime I could write a script to translate the pasted seq to jalview on-the-fly, which would be an ok workaround. I'll add yet another suggestion connected to the iupac symbols and that would be to have the option of using these for the nucleotide consensus row. / Jonas STATENS SERUM INSTITUT - 5, Artillerivej - DK-2300 Copenhagen S Tel: +45 3268 3268 - Fax: +45 3268 3868 serum@ssi.dk www.ssi.dk This e-mail, inclusive of attachments, is intended for the person(s) or entity stated above and may contain confidential information. Unauthorised reading, disclosure, copying, distribution or use of this information may violate rights to proprietary information. If you are not an intended recipient, please return this e-mail to the sender and delete your copy. Thank you. From JLR at ssi.dk Thu Jan 31 10:08:03 2008 From: JLR at ssi.dk (Jonas Larsson) Date: Thu Jan 31 10:08:20 2008 Subject: [Jalview-discuss] Copy raw sequence! In-Reply-To: <479F360B.2070906@compbio.dundee.ac.uk> References: <479F32EA.B062.0032.0@ssi.dk> <479F360B.2070906@compbio.dundee.ac.uk> Message-ID: <47A1AC13.B062.0032.0@ssi.dk> >>> On 29-01-2008 at 15:19, James Procter wrote: >> For my part the best thing would be to use ctrl-c for raw copy and ctrl-shift-c >> for fasta copy. This is of course not a good idea as a default for jalview >> since that would not be backwards compatible but one could always wish for >> two additions: raw copy on ctrl-shift-c as default and a checkbox in >> preferences to swap the two copy variants... >> >> As of now I am actually using MEGA in parallel with jalview just for this >> reason, quite inefficient but stripping out fasta headers all time was even >> worse :( > > I'd vote for having a preference (or something) for what jalview uses to > copy the data to the clipboard. The application doesn't even touch the > clipboard when copies occur internally so internal compatibility for the > CTRL-C behaviour isn't really an issue. Ah, no I meant more that people are used to gettnig the Fasta sequence and not the raw so changing default behaviour would maybe not be a good idea. / Jonas STATENS SERUM INSTITUT - 5, Artillerivej - DK-2300 Copenhagen S Tel: +45 3268 3268 - Fax: +45 3268 3868 serum@ssi.dk www.ssi.dk This e-mail, inclusive of attachments, is intended for the person(s) or entity stated above and may contain confidential information. Unauthorised reading, disclosure, copying, distribution or use of this information may violate rights to proprietary information. If you are not an intended recipient, please return this e-mail to the sender and delete your copy. Thank you.