tag:blogger.com,1999:blog-3172864904300737015.comments2022-03-27T12:56:24.454-07:00Bioinformatics made easyUnknownnoreply@blogger.comBlogger26125tag:blogger.com,1999:blog-3172864904300737015.post-18853341394956460702012-04-10T22:56:19.060-07:002012-04-10T22:56:19.060-07:00Thanks dear u make each and every posting awesome....Thanks dear u make each and every posting awesome.harishkumarhttps://www.blogger.com/profile/15574022894540307847noreply@blogger.comtag:blogger.com,1999:blog-3172864904300737015.post-36391225349360598202012-03-11T07:47:08.843-07:002012-03-11T07:47:08.843-07:00Its nicely made n I really liked it so much.It cou...Its nicely made n I really liked it so much.It could have ben better if the results and interpretation is more elaborateUnknownhttps://www.blogger.com/profile/11954936724336786523noreply@blogger.comtag:blogger.com,1999:blog-3172864904300737015.post-60763617017949000892012-02-29T02:31:38.533-08:002012-02-29T02:31:38.533-08:00Hi Kuhan, i'm really glad i helped. I myself p...Hi Kuhan, i'm really glad i helped. I myself prefer visual learning, especially live demonstrations. Good luck with your project, and thanks for your commentthe-shadowhttps://www.blogger.com/profile/10635712125175278091noreply@blogger.comtag:blogger.com,1999:blog-3172864904300737015.post-19990556834079113092012-02-29T02:21:20.955-08:002012-02-29T02:21:20.955-08:00hi, am new for bioinfomatics especially a.a sequen...hi, am new for bioinfomatics especially a.a sequencing, So i am self learning it for phd project. Reading a book from arthur lecks. But nothing beats your videos.... now i am playing compared to reading...thank you again.kuhanhttps://www.blogger.com/profile/11130124143201775507noreply@blogger.comtag:blogger.com,1999:blog-3172864904300737015.post-56645802172453706362011-12-26T00:22:51.113-08:002011-12-26T00:22:51.113-08:00There are actually many conversion tools available...There are actually many conversion tools available on the web. You can just do a Google search and it will return many of them. Here are some of them:<br /><br />http://genome.nci.nih.gov/tools/reformat.html<br /><br />http://hcv.lanl.gov/content/sequence/FORMAT_CONVERSION/form.html<br /><br />http://searchlauncher.bcm.tmc.edu/seq-util/Options/readseq.html<br /><br />You can choose whatever offers the output formats that you wish. Good luckthe-shadowhttps://www.blogger.com/profile/10635712125175278091noreply@blogger.comtag:blogger.com,1999:blog-3172864904300737015.post-74967735319667800282011-12-25T19:16:58.873-08:002011-12-25T19:16:58.873-08:00Hi there! Is there a tool to convert between these...Hi there! Is there a tool to convert between these formats? Please :) <br /><br />Thanks!Kinowhttps://www.blogger.com/profile/18261111481080669546noreply@blogger.comtag:blogger.com,1999:blog-3172864904300737015.post-48750395589487376182011-11-28T09:50:35.722-08:002011-11-28T09:50:35.722-08:00agree with you siragree with you sirmandar9smarthttps://www.blogger.com/profile/09033953752896648346noreply@blogger.comtag:blogger.com,1999:blog-3172864904300737015.post-9181624148715930212011-09-04T01:29:01.071-07:002011-09-04T01:29:01.071-07:00thanks .......thanks .......saboohttps://www.blogger.com/profile/12545813915861570423noreply@blogger.comtag:blogger.com,1999:blog-3172864904300737015.post-19401342881345016672011-06-22T07:51:57.653-07:002011-06-22T07:51:57.653-07:00Hello,
Thank you for the above video - was very he...Hello,<br />Thank you for the above video - was very helpful. <br />Can you make a video on the more accurate methods of forming a phylogenetic tree? That will be great. Kind regards.Miahttps://www.blogger.com/profile/01805626774441409231noreply@blogger.comtag:blogger.com,1999:blog-3172864904300737015.post-84345200776650031222011-04-27T07:26:01.986-07:002011-04-27T07:26:01.986-07:00Hello,
1- You can choose the Phylip format as an ...Hello,<br /><br />1- You can choose the Phylip format as an output before you do the alignment with ClustalW. This format is the one compatible with the Phylogeny inference package. In the "output" drop down menu, select Phylip as there are normally five formats that ClustalW exports to.<br />2- The other solution is to convert your existing format to Phylip format. You can just Google this phrase: ClustalW to Phylip and you'll find scripts where you can paste your format and convert it to Phylip format.<br /><br />When you get the Phylip format, you can use it to construct phylogenetic trees as i did in my video tutorial.the-shadowhttps://www.blogger.com/profile/10635712125175278091noreply@blogger.comtag:blogger.com,1999:blog-3172864904300737015.post-45339861254294472482011-04-26T15:16:04.060-07:002011-04-26T15:16:04.060-07:00How do I get the alignment shown at the end of thi...How do I get the alignment shown at the end of this video into a format that is useful in the PHYLIP program? If I just copy and paste the CLUSTAL 2.1 multiple sequence alignment that it gives me, the PHYLIP program won't work. How do I get my aligned sequences to look like the ones you used in your video on PHYLIP? If you could e-mail me an answer that would be greatly appreciated! jguter@middlebury.edu<br />Thanks you!Unknownhttps://www.blogger.com/profile/07055942376183935525noreply@blogger.comtag:blogger.com,1999:blog-3172864904300737015.post-25840939176634312072011-02-25T23:47:56.591-08:002011-02-25T23:47:56.591-08:00Hello, honestly i didn't try it. But i think i...Hello, honestly i didn't try it. But i think it could work for you if you have a processor which supports 64b, but probably you may face memory problems. It doesn't take too long to try it, so i advise you to do so and see what comes after and let us know if it worked or not. Good luckthe-shadowhttps://www.blogger.com/profile/10635712125175278091noreply@blogger.comtag:blogger.com,1999:blog-3172864904300737015.post-78228208205015093612011-02-25T15:21:08.070-08:002011-02-25T15:21:08.070-08:00This method (option 4) functions with Biolinux 6 (...This method (option 4) functions with Biolinux 6 (64b) in a Vista Ultimate (32b) operating system?Cristianhttps://www.blogger.com/profile/15913354997633480076noreply@blogger.comtag:blogger.com,1999:blog-3172864904300737015.post-1048005411663986752010-11-22T02:55:16.388-08:002010-11-22T02:55:16.388-08:00You are absolutely right, each of the programming ...You are absolutely right, each of the programming languages has its own advantages and disadvantages, i'm just suggesting that PERL is a very good programming language especially for beginners, may be in an other post i'll explain in details the advantages and disadvantages of using each programming language in Bioinformatics.the-shadowhttps://www.blogger.com/profile/10635712125175278091noreply@blogger.comtag:blogger.com,1999:blog-3172864904300737015.post-33177174307789813172010-11-22T02:32:04.535-08:002010-11-22T02:32:04.535-08:00It would have been nice if you could have compared...It would have been nice if you could have compared the different languages you mentioned for each of their merits so that the reader could have made up his/her own mind. Especially since there is also BioPython, BioJava, and BioRuby so the point about BioPerl is less impressive. <br /><br />Besides, each language has it's own merits and flaws, so it largely depends on the application as to which language you choose.Wesley Harrisnoreply@blogger.comtag:blogger.com,1999:blog-3172864904300737015.post-46273317392892741652010-11-11T22:46:09.562-08:002010-11-11T22:46:09.562-08:00Excellent and informative blog. Thanks for posting...Excellent and informative blog. Thanks for posting this. It’s informative and enlightening. <br /><a href="http://www.memxbio.com" rel="nofollow">Membrane Protein Structure</a>tobeyhttps://www.blogger.com/profile/08377356977450137656noreply@blogger.comtag:blogger.com,1999:blog-3172864904300737015.post-48173121694047644912010-09-21T06:13:41.128-07:002010-09-21T06:13:41.128-07:00You are absolutely right, the advancements made in...You are absolutely right, the advancements made in bioinformatics will include every area in biology and medecine and even more. thanks for the commentthe-shadowhttps://www.blogger.com/profile/10635712125175278091noreply@blogger.comtag:blogger.com,1999:blog-3172864904300737015.post-43528411525167085712010-09-20T23:21:19.505-07:002010-09-20T23:21:19.505-07:00Bio informatics links most to the biology branches...Bio informatics links most to the biology branches...today bio informatics is making huge advancement..Bio informatics is developed and structured to integrate engineering with medicine<br />to solve our health related problems and enhance our quality of life. Bio-Medical Engineering being a relatively new multidisciplinary areajasmine25http://www.genebyte.firm.in/noreply@blogger.comtag:blogger.com,1999:blog-3172864904300737015.post-6847301711106267922010-09-10T02:11:17.262-07:002010-09-10T02:11:17.262-07:00You are welcome my friend, any time.You are welcome my friend, any time.the-shadowhttps://www.blogger.com/profile/10635712125175278091noreply@blogger.comtag:blogger.com,1999:blog-3172864904300737015.post-13586517308639250942010-09-09T11:10:07.760-07:002010-09-09T11:10:07.760-07:00you ar the best man.................
I want to be ...you ar the best man.................<br />I want to be ur student...............Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-3172864904300737015.post-75522766382185891052010-09-09T06:30:01.080-07:002010-09-09T06:30:01.080-07:00Hi, i know some methods, all you have to do is to ...Hi, i know some methods, all you have to do is to go to the MIPS database, in the field X-Ref (cross references) you enter the name of the database (abrv) and the accession number, example: sp:P21575 , this means the database Swissprot and the accession number P21575.<br />sp: swissprot<br />gb: Genbank<br />pir: PIR<br /><br />For SCOP it contains the same entries of PDB, so you'll find the swissprot reference and identifier in the header file.the-shadowhttps://www.blogger.com/profile/10635712125175278091noreply@blogger.comtag:blogger.com,1999:blog-3172864904300737015.post-36783917135885818072010-09-08T10:56:00.697-07:002010-09-08T10:56:00.697-07:00Hi, nice article,
I am having a question about pro...Hi, nice article,<br />I am having a question about protein networks,<br />do you know any methode how to find cross-reference from MIPS to SwissProt and from from SwissProt to SCOP<br /><br />My mail is djek.nad AT google DOT comAnonymousnoreply@blogger.comtag:blogger.com,1999:blog-3172864904300737015.post-12730786933939489082010-07-18T05:45:18.983-07:002010-07-18T05:45:18.983-07:00You are absolutely right, but in my experience, PE...You are absolutely right, but in my experience, PERL is the easiest and the most efficient one. It's installed in almost all Linux distributions and you can install it in windows if you want. With the addition of BioPERL and it's magnificent libraries, you'll become an invincible Bioinformatician!!!, thanks for the comment and good luck.the-shadowhttps://www.blogger.com/profile/10635712125175278091noreply@blogger.comtag:blogger.com,1999:blog-3172864904300737015.post-58995536907457805502010-07-17T12:02:14.621-07:002010-07-17T12:02:14.621-07:00use the right regular expression library and you h...use the right regular expression library and you have pattern detection capabilities in ANY of those languagesAnonymousnoreply@blogger.comtag:blogger.com,1999:blog-3172864904300737015.post-64187237786190690642010-03-15T03:48:22.723-07:002010-03-15T03:48:22.723-07:00OK thanx for the comment, but this tutorial is a b...OK thanx for the comment, but this tutorial is a basic tutorial that describes distance methods, i know that most bioinformaticians use Likelyhood methods which are the most accurate, but some friends asked me to post a basic phylogenetic trees building method. if you have any suggestions don't hesitate, thanx.the-shadowhttps://www.blogger.com/profile/10635712125175278091noreply@blogger.com