<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; ">Hi Koen<BR><DIV><DIV>On Aug 10, 2006, at 6:34 PM, Koen van der Drift wrote:</DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Hi Davide,</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Welcome to BioCocoa! It would be great if the framework will be used in a proteomics app.<SPAN class="Apple-converted-space"> </SPAN></DIV></BLOCKQUOTE><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Well, I have some ideas but, as I said, I'm pretty new to Cocoa programming, so you have to give me time to understand a lot of things... :-)</DIV><BR><BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">What I understand, formatdb is a standalone CLI app, correct? We need to look into if we can add this (because of possible license issues). Otherwise, we can write our own class, based on the formatdb source code. I encourage you to look into that possibility, we can help here to convert it to Objective-C and Cocoa.</DIV></BLOCKQUOTE><DIV><BR class="khtml-block-placeholder"></DIV><DIV>I'm thinking about reading the code of fastacmd utility instead of formatdb, as fastacmd does read blast formatted databases and can extract some info (whole sequences, accession numbers only, get only a sequence or the entire database...). I'll take a look then to the source code, then</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>d</DIV><DIV><BR class="khtml-block-placeholder"></DIV><BR><BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">cheers,</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">- Koen.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">-----Original Message-----</DIV> <BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">From: Davide Cittaro <<A href="mailto:davide.cittaro@ifom-ieo-campus.it">davide.cittaro@ifom-ieo-campus.it</A>></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Sent: Aug 10, 2006 11:32 AM</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">To: BioCocoa Mailinglist <<A href="mailto:biococoa-dev@bioinformatics.org">biococoa-dev@bioinformatics.org</A>></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Subject: [Biococoa-dev] Reading blast formatted files</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Hi there, I'm new to BioCocoa (well, I've discovered it yesterday) <SPAN class="Apple-converted-space"> </SPAN></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">and pretty new to Cocoa programming. I would like to start using this <SPAN class="Apple-converted-space"> </SPAN></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">framework for some proteomics app.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">I would like to know if there is a way to read database formatted for <SPAN class="Apple-converted-space"> </SPAN></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">NCBI blast with formatdb. Ok, I'm also going to read the documentation!</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">d</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">/*</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Davide Cittaro</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">HPC and Bioinformatics Systems @ Informatics Core</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">IFOM - Istituto FIRC di Oncologia Molecolare</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">via adamello, 16</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">20139 Milano</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Italy</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">tel.: +39(02)574303355</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">e-mail: <A href="mailto:davide.cittaro@ifom-ieo-campus.it">davide.cittaro@ifom-ieo-campus.it</A></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">*/</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV> </BLOCKQUOTE><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV> </BLOCKQUOTE></DIV><BR><DIV> <SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Lucida Grande; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Lucida Grande; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Courier New; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ; font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; ">/*</SPAN></SPAN></SPAN></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ; font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; ">Davide Cittaro</SPAN></SPAN></SPAN></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ; font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; ">HPC and </SPAN></SPAN><SPAN class="Apple-style-span" style="font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; ">Bioinformatics Systems @ Informatics Core</SPAN></SPAN></SPAN></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; ; font-family: Helvetica; "><BR style="font-family: Helvetica; "></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ; font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; ">IFOM - Istituto FIRC di Oncologia Molecolare</SPAN></SPAN></SPAN></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ; font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; ">via adamello, 16</SPAN></SPAN></SPAN></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ; font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; ">20139 Milano</SPAN></SPAN></SPAN></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ; font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; ">Italy</SPAN></SPAN></SPAN></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; ; font-family: Helvetica; "><BR style="font-family: Helvetica; "></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ; font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; ">tel.: +39(02)574303355</SPAN></SPAN></SPAN></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ; font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; ">e-mail: <A href="mailto:davide.cittaro@ifom-ieo-campus.it">davide.cittaro@ifom-ieo-campus.it</A></SPAN></SPAN></SPAN></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ; font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; ">*/</SPAN></SPAN></SPAN></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ; font-family: Helvetica; "><BR class="khtml-block-placeholder"></DIV><BR class="Apple-interchange-newline"></SPAN></SPAN></SPAN></SPAN></SPAN> </DIV><BR></BODY></HTML>