L1Xplorer
Detection and Annotation of Full-Length, Intact L1 Elements
 

Update 2015/03/06:

L1Xplorer is back online after a brief server hiccup. If you still experience issues we are happy to help (penzkofert (at) gmail.com).

What is L1Xplorer?

L1Xplorer is a web-frontend to the perl suite we developed to automatically detect and annotate L1s. Here you can paste your sequence and see if there are full-length, intact L1s present and see the classification features that can be found on them. Although this system works to an extent with scattered LINE-1s, the reliable results will be found with almost full-length L1s. To look for pieces of L1s we recommend www.repeatmasker.org.

If you are experimentalists and you seek a bioinformatics expertise on analysis of LINE-1 elements, do not hesitate to send us an email!

If you are using L1Xplorer for your research please cite L1Base: from functional annotation to prediction of active LINE-1 elements Nucl. Acids Res. 2004 33: D498-D500; doi:10.1093/nar/gki044

Species:

Input sequence
 


Sequence name



Paste sequence


or upload file

(5 megabases limit)

Example Searches:
- Human L1.3 results (query)

 

 


 

Classification modules
 

Search Sequence:

General

ORF1 %A
ORF2 %A
ORF2 %T
ORF1&2 %A
PolyA Signal
ORF1 %T
ORF1&2 %T
CPG Islands
Poly-A
Kimura dist. to L1.2
G-C Content
find TSDs

Family

Ta SSVs
Ta1-nd/d
Ta0/Ta1 SSVs
L1M/L1PA Discrimination

Promoters

SRY Site 2
SRY Site 1
Runx3 ASP
Runx3 Site
YY1 BoxA+BoxA
Runx3 Site 2

Activity

HMKK1091
ARR260
D145
TF nkx-2.5
SSS1096
N14
Y115
ORF StartStop
E43
ORF1 CAI
I1220
T192
R363
SDH228
REKG235
YPAKLS282
D205
ORF2 CAI
N147
TF nkx-2.5B
FADD700
S1259

Intactness

Intactness Score
  
 


Filtering options
 
Those filters (if active) are applied during detection process:
  • % of coverage of ORF1 and must not have frameshifts/stopcodons
  • % of coverage of ORF2 and must not have frameshifts/stopcodons

 

 


Advanced Options

 


  • Maximal evalue for a HSP to be included:
  • coverage of query sequence: %
  • HSP distance to cluster unconditionally:
    maximum HSP distance to cluster conditionally:
    with max angle of deg. and min angle of deg. (more info...)
  • minimal TFASTX score for detected ORF:
  • Extend locus:
    do not extend
    based on relative position of locus (extend up to borders of query sequence plus values given below)
    based on absolute borders of L1 hit locus (extend blindly by values given below)
    by nt on 5' border and nt on 3' border

 

 

Tomasz Zemojtel, Institute for Molecular Genetics, Max-Plack Institute Berlin
Tobias Penzkofer, Department of Bioinformatics, University of Würzburg