University of Bielefeld - Technische Fakultaet - Praktische Informatik - R I F L E - Request Form

R I F L E

Rapid Identification by Fragment Length Evaluation - Request Form

This document is intended for routine use of the RIFLE system. To provide detailed usage information, all headlines are links to the appropriate sections of the
[DOC] user manual

Databases

The RIFLE system compares your restriction patterns to theoretical restriction patterns which are generated from 16S rDNA databases. Please select at least one of the following databases:

Halophila stipulacea-associated microorganisms
RDP unaligned sequences, June 1995

Primer

Please select the primer pair used in your laboratory:

Experimental artefacts

Some laboratory processes produce additional sequences before or after the 16S rDNA primers, e.g. vector sequences. Please indicate the length of these sequences. The RIFLE system will suppose that these sequences aren't cut by the selected restriction enzymes. So their length will be added to the length of the first/last fragment of the 16S rDNA.

base pairs before the forward primer
base pairs after the reverse primer

Restriction patterns

To improve the quality of identifications, the results of multiple digests of one strain with different enzymes can be combined. If you activate the following button, restriction patterns with the same second number, e.g. 0.2 and 1.2, will be considered as different digests of the same strain, the results will be combined.
Restriction patterns with the same number originate from the same strain

Missing data

(Only if you have activated the previous option)

Due to poor database sequence quality, restrictions pattern data may be missing for some sequence-enzyme combinations. If you activate the following button, these organisms will not be listed in the "Combined results" section.
Organisms for which restriction pattern data is missing for some of the selected enzymes are skipped.

EnzymeNumberName (optional)Restriction pattern
Example: Ecoli K12Example: 70 357 90 460 266
0.0
0.1
0.2
0.3
0.4
1.0
1.1
1.2
1.3
1.4
2.0
2.1
2.2
2.3
2.4
3.0
3.1
3.2
3.3
3.4

Laboratory resolution

Fragments shorter than
base pairs will be ignored in the theoretical patterns.

Subsequent theoretical fragments whose length difference is smaller than
% of the length of the shorter fragment will be considered as one fragment.

Filtering of results

Only organisms with an edit distance of at most
base pairs to the laboratory pattern will be displayed.

Only the
organisms with the smallest edit distances will be displayed.

Reply mode

Interactive
Email

Personal data

Name (optional)

Institution (optional)

Email

The processing time of a request is several minutes. The estimated processing time of your request will be displayed immediately.
Henning Hermjakob, bibi-help(at)techfak.uni-bielefeld.de, 1998-01-07