MegaLTR Web Server

MegaLTR Documentation Contact

Intact LTR-RT identification and annotation of internal domains

Input Files

Fasta File [Please provide compressed (.zip; .gz) or uncompressed fasta file (.fasta; .fa; .fna). *Required ]. Download sample FASTA file

Fasta File link (NCBI ftp link only)

Please note that when uploading or providing FTP links for large genome sequences, we prefer to use Google Chrome rather than Firefox

LTR-retrotransposons identification

Minimum LTR Length Minimum distance between LTRs Maximum divergence between terminal repeats (%)

Maximum LTR Length Maximum distance between LTRs Minimum length of exact match pair

Select Species *If your species is not found please select the closet species

Annotation of internal domains

Mininum coverage for protein domains in HMMScan Maxinum E-value for protein domains in HMMScan

TE Database that TEsorter will use it

HMM-database that TEsorter will use it

Classifying rule [identity-coverage-length] based on similarity

If you want to recieve the results once processing is finished, please enter your email. (OPTIONAL)

Note: Files greated than 100MB might take long time.

Intact LTR-RT Identification and annotation of internal domains plus determination of insertion time

Input Files

Fasta File [Please provide compressed (.zip; .gz) or uncompressed fasta file (.fasta; .fa; .fna). *Required ]. Download sample FASTA file

Fasta File link (NCBI ftp link only)

Please note that when uploading or providing FTP links for large genome sequences, we prefer to use Google Chrome rather than Firefox

LTR-retrotransposons identification

Minimum LTR Length Minimum distance between LTRs Maximum divergence between terminal repeats (%)

Maximum LTR Length Maximum distance between LTRs Minimum length of exact match pair

Select Species *If your species is not found please select the closet species

Annotation of internal domains

Mininum coverage for protein domains in HMMScan Maxinum E-value for protein domains in HMMScan

TE Database that TEsorter will use it

HMM-database that TEsorter will use it

Classifying rule [identity-coverage-length] based on similarity

Insertion age estimation

Evolution rate

To convert the evolution rate to decimal number use the follwing site https://calculator.name/scientific-notation-to-decimal/1.5e-8

If you want to recieve the results once processing is finished, please enter your email. (OPTIONAL)

Note: Files greated than 100MB might take long time.

Intact LTR-RT Identification, annotation of internal domains [Part A], determination of insertion time [part B], LTR-RT gene-chimera analysis and visualization of gene density and LTR-RTs across chromosomes

Input Files

Fasta File [Please provide compressed (.zip; .gz) or uncompressed fasta file (.fasta; .fa; .fna). *Required ]. Download sample FASTA file

Annotation File [Please provide compressed (.zip; .gz) or uncompressed annotation file (.gff; .gff3). *Required for LTR-gene chimeras detection and nearby genes detemination]. Download sample GFF file

Fasta File link (NCBI ftp link only) Annotation file link (NCBI ftp link only)

Please note that when uploading or providing FTP links for large genome sequences, we prefer to use Google Chrome rather than Firefox

LTR-retrotransposons identification

Minimum LTR Length Minimum distance between LTRs Maximum divergence between terminal repeats (%)

Maximum LTR Length Maximum distance between LTRs Minimum length of exact match pair

Select Species *If your species is not found please select the closet species

Annotation of internal domains

Mininum coverage for protein domains in HMMScan Maxinum E-value for protein domains in HMMScan

TE Database that TEsorter will use it

HMM-database that TEsorter will use it

Classifying rule [identity-coverage-length] based on similarity

Insertion age estimation

Evolution rate

To convert the evolution rate to decimal number use the follwing site https://calculator.name/scientific-notation-to-decimal/1.5e-8

LTR-gene chimeras & nearby genes determination

The distance to the LTR-retrotransposons in base pair.

Upstream

Downstream

Genes and LTR-RTs density visualization

Window size

Number of chromosomes

If you want to recieve the results once processing is finished, please enter your email. (OPTIONAL)

Note: Files greated than 100MB might take a long time.

To run an example, please use the Fasta and GFF files for chromosome # 1 of Arabidopsis thaliana, NCBI accession "NC_003070.9". The sequence is 30,427,671 bp and the analysis takes between 30 to 40 minutes, depending on the number of jobs running.

MegaLTR: A web server for LTR-retrotransposons analysis in high-throughput data scale

Intact LTR-RT identification and annotation of internal domains

Input Files

LTR-retrotransposons identification

Annotation of internal domains

Intact LTR-RT Identification and annotation of internal domains plus determination of insertion time

Input Files

LTR-retrotransposons identification

Annotation of internal domains

Insertion age estimation

Intact LTR-RT Identification, annotation of internal domains [Part A], determination of insertion time [part B], LTR-RT gene-chimera analysis and visualization of gene density and LTR-RTs across chromosomes

Input Files

LTR-retrotransposons identification

Annotation of internal domains

Insertion age estimation

LTR-gene chimeras & nearby genes determination

Genes and LTR-RTs density visualization