iHMMune-align web-based accessHelp, FAQs and Further Information |
FAQ: OutputHow do I work with the CSV output?It depends on what you want to do! The output isn't pretty but it is far more functional than a pretty HTML display that can be difficult to parse because of all the tags and formatting. The CSV file can easily but imported into spreadsheet programs such as Microsoft Excel where you can use the functions such as pivottables to look at features of a set of input sequences. If you want to import the CSV file obatined from iHMMune-align you can just open it up in Notepad/TextEdit (or any similar text editor) and then cut and paste into excel. If you select the 'Text Import Wizard' when you paste the text and then select semi-colon as the file delimiter everything will eand up in its own cell. The CSV file can also be easily parsed using your favourite scripting language or loaded up into an SQL database. What do the '.' in the CSV output represent?The '.' which may appear at the start/end of the gene segments indicate exonuclease removals relative to the germline sequence. I have many hundreds/thousands of sequences that I want to partition. Is there a faster way?Obviously the web interface isn't ideal for these applications. A version of iHMMune-align that will run on you local machine can be downloaded by following the 'Download' link under the 'Main' section of the side-bar menu. iHMMune-align is implemented in Java so will run on any OS that has JVM running. The download includes some useful perl scripts for use with iHMMune-align, including a script that allows limitless sequences to be run in batch. The HMM can get a little memory hungry so is best run on machines with at least 1Gb of memory for optimum performance (has been run on a laptop with only 384Mb). |
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