Convert between sequence and cytogenetic coordinates

This tool is meant to help you convert between sequence and cytogenetic coordinates. You can upload a file of sequence locations and we'll return the cytogenetic band that location maps to; alternatively, you can upload a list of cytogenetic bands and we'll provide the sequence locations for those bands. By default, files are named 'conversion.tsv'.

Using this page

To start, you must first choose an organism from the pull-down menu labeled 'Organism:'. Next, select an assembly from the 'Assembly:' pull-down menu.

Converting from sequence to cytogenetic coordinates

Select the button next to 'Sequence to Cytogenetic'.

Then, upload your file. You can provide data in the following ways

  • A list of Features
    • A list of gene symbols
    • A list of RefSeq transcript IDs
    • A list of SNP IDs
  • Standard annotation files
    • A BED file
    • A GFF/GTF/GVF file
    • A VCF file

If you provide data as a list of features, we will return a file that lists the provided features and their cytogenetic location. If you provide a feature list, the output file will contain the list of features with a new column with the cytogenetic location will be appended. For example:

Input:

CFTR

Output:

CFTR    7q31.2

If you provide an annotation file, a four column, tab-delimited file will be returned.

col1: chromosome
col2: start
col3: stop
col4: cytogenetic band

Converting from cytogenetic to sequence coordinates

Select the button next to 'Cytogenetic to Sequence'.

Then, upload your file; this should just be a list of cytogenetic locations.

Input:

7q31.2

Output: A four column file, tab delimited file, will be returned:

7    114600001    117400000     7q31.2

col1: chromosome
col2: start
col3: stop
col4: cytogenetic band

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Last updated: 2013-07-10T09:55:10-04:00