Therefore, these types of datasets are valuable references when attempting to taxonomically classify T-RF peaks from diverse microbial communities. Tools have been previously developed to perform in silico digestions of 16S rRNA gene sequences and/or to assign a taxonomic label to the chromatograms. Such programs include TAP-TRFLP [10], MiCA [11], PLX3397 T-RFLP Phylogenetic Assignment Tool (PAT; [12]), TReFID [13], TRAMPR [14], an ARB-software integrated tool [15] and TRiFLe [16]. Table 1 contains

some of the essential features of these packages. The most obvious advantage of T-RFPred as compared with other available software applications is that the program handles either partial or full-length user input NU7441 datasheet sequences. This is because T-RFPred retrieves complete sequences of close relatives from the public databases for T-RF assignments and at the same time it taxonomically bins the clone sequences. Furthermore, it can use large LY294002 cell line sequence datasets of virtually any size as reference sets in taxonomic assignments. T-RFPred is exclusive to 16S rRNA gene sequences and designed to exploit the full potential of T-RFLP profiles and their use in the description of prokaryotic communities. Table 1 Characteristics of the available software to assign a phylogenetic label to the chromatogram fragment peaks Software package Characteristics Reference TAP-TRFLP

Amoxicillin Web-based. Although it can be accessed through the older version of the Ribosomal Database Project, it has not been updated. [10] MiCA Web-based. Newest version (MiCA 3) allows the selection of primers and in silico digestion of database sequences. Does not allow for user input sequences.

[11] T-RFLP Phylogenetic Assignment Tool (PAT) Web-based. Contains database of terminal restriction fragment sizes. Allows for the upload of fragment size database. [12] TReFID Downloadable. Databases include 16S rRNA gene, dinitrogenase reductase gene (nifH) and nitrous oxide reductase gene (nosZ). Limited number of sequences although the user could expand it. [13] TRAMPR R package. Based on a database of known T-RFLP profiles that can be constructed by the user. Loads data directly from ABI output files. Allows analysis with any type of gene, primer set and restriction enzyme. [14] ARB-software integrated tool (TRF-CUT) Part of the ARB software. Allows for user input sequences that need to be aligned before analysis. Any type of gene could be analyzed. [15] TRiFLe Java based. Allows for user input sequences. Can analyze any type of gene. [16] T-RFPred Handles large database, such as 16S rRNA sequences from metagenomes, of user input clone sequences that do not need to be full length; multiple platforms. Makes use of the Ribosomal Database Project sequence database, which updates regularly. User needs to install Perl, Bioperl, BLAST and EMBOSS.