How To Compare The 454 Vs Illumina Sequences

Question

[deepthithomaskannan]

Hi all,

Sorry for the misunderstanding.I am elaborating the question below.

I have 454 sequences and illumina sequences for same animal samples. Using illumina sequence processing I have found some interesting patterns relevant to our problem. I would like to search the presence of those interesting illumina sequences in 454 animal sample sequences so that I can find which are the 454 animals having a hit in interesting illumina sequences. I would like to know which method is more suitable to check illumina against 454 sequences or vice versa. illumina sequences are shorter than 454 sequences.

Thanks, D.

Answer 1

[Istvan Albert]

It is not clear what you mean exactly - there are many papers comparing sequencing platforms, see this post: Sequencing technology review papers

Answer 2

[vijay]

Could you please elaborate on what context you would like to compare these two platforms. Each of them has their own merits and demerits. are you looking forward to choose one among them for your sequencing purpose??

[deepthithomaskannan]

I have 454 sequences and illumina sequences for my samples. I would like to search the presence of some interesting illumina sequences in 454 sequences.

[vijay]

I would suggest to go for a filter based on the length of those interesting sequences from both datasets ..hope it would give an idea if both the datasets contain them(unless they are equal). else you can perform a pattern search which a substring of your 454 sequence in the illumina data....

you can store those sequences separately in a file and quickly run a grep over it against illumina file!!!

Answer 3

[SES]

You could start by using FastQC or PRINSEQ to summarize and compare your data. I can tell you that GC content is one area where your data will differ, in my experience. The papers Istvan linked to will describe the technical differences between the platforms. If you are wanting to get an idea of how similar the two sets are, I would start with taking a subset of each and comparing them with Vmatch, which is a very flexible tool for comparing sequence data sets.