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This section will explain the all parameters in Somatic Motif online tool and how to interpret results.
Common Parameters.
To find somatic motif by sequence.
To find somatic motif by genomic interval.
To extract all somatic motifs.
Check against existing database.

Common Parameters

Parameters

Explanation

Upload Mutation File

Upload a mutation file in CVS format including five columns. The first column reprsents the chromsome name of species or name for SARS genomes. All chromosomes were supported in this web. The second column reprsents the location of somatic mutation/SNP in genomes. The third column reprsents the reference nucleotide of mutation site. The forth and fifth columns reprsent the two mutation/SNP nucleotide of mutation site. Additional, altered binding sequences can arise from single nucleotide mutations, insertion, deletion, RNA editing, or SNP. Additional, Four projects were supported in this web. A sample file was supplied in below. Where, "-" symbol in sample file reprsents deletion.

Select a Genome

Select a species from drop down menus. SomaticMotif covers 28 genomes from 26 species , in which supports 19307 SARS genomes.

MEME Output

Whether output MEME format file for sequence of somatic motif.

Additional Annotation

Whether annotate the mutation/SNP location. It is only work for Human GRCh37 and GRCh38.

Email (optional)

Due to long runtime, results will be emailed to you.

To find somatic motif by sequence

1.Function:

All sequence altering mechanisms may result in gain or loss of important motifs. Somatic Motif online tool can be used to annotate and identify altered binding motifs, including transcription factors, RNA binding protein sites et al.

2.Parameters:

Parameters

Explanation

Motif sequence

A single DNA nucleotide sequence can input into the text box. Similar to single sequence, when multiple sequences are to be input, FASTA and MEME format file can be uploaded using the Upload File button. Mutations in mutation file are checked against reference FASTA to determine if any of the uploaded sequences is produced due to mutations.

Somatic Motif Type

To extract gained or lost important motifs from genome.

Adjacent Mutations

Whether consider the multiple alternative sequences generated by multiple adjacent mutations.

3.Interpretation of results:

Results

For example: we upload mutation sample file and input "TTCCGG" sequence and choose Somatic Motif Type as Gain and Loss. The result is as following:

Interpretation of Results

The mutation on position 1295228 of chromosome 5 of G>T at the '-' strand forms a new binding motif sequence TTCCGG.

To find somatic motif by genomic interval

1.Function:

Mutation in mutation file is checked against reference FASTA to determine if any of the sequences of genomic interval is produced. For example, a miRNA seed region file can be used as an input to determine any miRNA seed sequence has been produced by mutations.

2.Parameters:

Parameters

Explanation

Genomic interval file

Genomic interval file can be uploaded using the Upload File button. It is similar to BED format but with five columns: chromosome, start, end, strand and ID.

3.Interpretation of results:

Results

For example: we upload mutation sample file and "hsa37.bed.csv" file in miRNA seed page. The result is as following:

Interpretation of Results

The Mutation on position 172089193 of chromosome 5, caused hsa-miR-5003-5p seed CA[C]AACA to become CA[A]AACA.

To extract all somatic motifs

1.Function:

Identify all possible somatic motifs based on input somatic mutations. Sequence length can be defined by user.

2.Parameters:

Parameters

Explanation

Identify all somatic motifs

length of sequence can be selected by user. For single nucleotide mutation, if 5 is chosen, a motif or sequence of length 11 will be generated.

3.Interpretation of results:

Results

For example: we upload mutation sample file and choose the length of sequence as 5. The result is as following:

Interpretation of Results

The mutation on position 12829679 of chromosome 5 of G>A at the '+' strand forms a new 11mer binding motif sequence TTTAC[A]AAAAG.

Check against existing database

1.Function:

Identify all possible somatic motifs based on existing database.

2.Interpretation of results:

Results

For example: we upload mutation sample file and choose RBPDB databse. The result is as following:

Interpretation of Results

The mutation on position 12829679 of chromosome 5 of G>A at the '+' strand forms a new PABPC1 gene binding motif sequence "AAAAA".