Locating Indels In Gene

Question

[bioinfo]

I have a excel file from windows (spreadsheet) contains start, end and indel sequences (-GGC means GGC deletion or +AAC means AAC insertion) in column 1, 2 and 3 respectively. I have a reference genome in both fasta format and EMBL format (annotated). How can I locate my indels in the genome based on reference? I want to find where eaxctly my indels are (e.g. in which gene or intergenic regions?)

e.g. my file

Start       End      Indel_Description
  12        20        +GCCGCAC
  45        46        -C

[Sean Davis]

What genome? Do you have the positions of genes in the genome (base pair locations?

[bioinfo]

Bacterial genome...I have the positions of all genes. Now I have to compare my indel positions to allocate genes..!!

Answer 1

[Sean Davis]

You can take a look at using bedtools if you want a command-line solution or the GenomicRanges package from Bioconductor to do genomic overlaps. Any Galaxy server can do these types of overlaps, also.

[bioinfo]

I prefer command line..I will have a go with your options though I haven't used bioconductor before. Any other solutions with regular perl script?

[Sean Davis]

You will probably need to write something in perl (or some other language) to convert to BED format if you want to use bedtools. I do know know of a perl script that does what you are asking for.

[bioinfo]

The excel file I mentioned above is actually the indel file in BED format. I have the annotated EMBL file of my genes. I have planned to convert the Embl file to gff format and then gff to BED format as of the BIoStart experts suggested. Then I will use the BEDtools to check the overlaps between these two BED files. I was wondering if there is any extra column in my genes.bed file compared to just 3 columns in indel.bed file will that work? or my genes.bed file should have exactly three columns like Indels.bed file to check the overlapping?

[Sean Davis]

See the bedTools manual for details, but bedTools supports GFF and several flavors of BED format.