Category: Software

Metaxa updated

Just a short note; Metaxa has been updated to version 1.0.1. This incremental version brings two small new features, and a minimal bug fix.

  • Added the option to select whether HMMER’s heuristic filtering should be used or not. This can be configured using the –heuristics option:
    –heuristics {T or F} : Selects whether to use HMMER’s heuristic filtering, off (F) by default
  • Removed some redundant information written to the screen, as output to the screen was a bit cluttered.

Bug fix:

  • Fixed a rare bug affecting detection sensivity of some SSU sequences.

Of course I would recommend it to every Metaxa user as it fixes a small bug, but the update is not in anyway critical for normal use.  The updated version can be downloaded using this link.

Metaxa released

I proudly announce that today Metaxa has been officially released. Metaxa is a a software tool for automated detection and discrimination among ribosomal small subunit (12S/16S/18S) sequences of archaea, bacteria, eukaryotes, mitochondria, and chloroplasts in metagenomes and environmental sequence datasets. We have been working on Metaxa for quite some time, and it has now been in beta for about two months. However, it seems to be stable enough for public consumption. In addition, the software package is today presented in a talk at the SocBiN conference in Helsinki.

A more thorough post on the rationale behind Metaxa, and how it works will follow when I am not occupied by the SocBiN conference. A paper on Metaxa is to be published in the journal Antonie van Leeuwenhoek. The  software can be downloaded from here.

Software reorganisation

I have reorganised my Software page a little bit, putting the smaller scripts on a separate page, to make the main software page tidier. The content of the pages is the same, and you still find bloutminer and metaorf on the main software page.

BLAST-mining software: bloutminer

I have put some “new” software online. I have had this piece of code lying around for some time but never got to upload it as I didn’t view it as “finished”. It is still not finished, but I would nevertheless like to share it with a wider audience. So, today I introduce bloutminer – the BLAST output mining script I have been using lately. bloutminer allows you to specify e.g. an E-value cutoff, a length cutoff and a percent identity cutoff, and extract a list of the hits satisfying these cutoffs. It takes table output (blastall option -m 8 ) as input. This is the software I used for the BLAST visualisation I have discussed earlier.

I normally use an E-value cutoff of 10 for my BLAST searches, and then extracts hits with bloutminer, allowing me to change the cutoffs at a later stage without redoing the whole BLAST search. You can also “pool” sequences into groups, based on their sequence tags. bloutminer is work in progress, and may contain nasty bugs. It can be found on the Software page. Please improve it at will.

Blastgrep updated

I have fixed two small bugs in the blastgrep tool (see below), and the version number has been increased to 1.0.2. This update is recommended to everybody who downloaded the previous version of blastgrep. The new version of blastgrep can be downloaded using this link.

Version 1.0.2 fixes:
  • Fixed a bug with extracting information from queries without any matches
Version 1.0.1 fixes:
  • Fixed an inconsistency bug while using “-o count”

Software: blastgrep

I have added some software I have written to this page (see link to Software at the top of the page). Among these is the useful little Unix/Linux utility blastgrep, which functions as a grep adopted for extracting useful information from BLAST-reports. I wrote it recently as I increasingly use complicated combinations of piped Unix-commands to do the same thing. blastgrep makes it all more easy. Use it as you wish, and if you do, please tell me about its bugs (hopefully none…)