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Search: Posts Made By: Jordy224
Forum: Bioinformatics 11-22-2010, 04:24 PM
Replies: 2
Views: 2,371
Posted By Jordy224
gsAssembler - predicted genome size?

Hello a I have a quick question concerning "newbler" gsassembler(v2.3). Can anyone suggest how to find the predicted genome size from the output of a de novo assembly?

To calc the n50 stat the...
Forum: General 11-02-2010, 05:50 PM
Replies: 4
Views: 3,751
Posted By Jordy224
I currently use the protein cluster application...

I currently use the protein cluster application in NCBI
For example:

http://www.ncbi.nlm.nih.gov/proteinclusters/624653

Notice there are multiple names for this single protein, and yet the...
Forum: General 10-29-2010, 10:21 PM
Replies: 4
Views: 3,751
Posted By Jordy224
Identifying gene name synonyms

A quick question.
Using Entez database or AmiGO, How to you find all synonyms of a particular gene in other genomes without falling back on a sequence homology search.

For example. Gene psaB...
Forum: 454 Pyrosequencing 03-28-2010, 09:07 PM
Replies: 3
Views: 2,943
Posted By Jordy224
great... The assembly finished in 13 hours: ...

great...
The assembly finished in 13 hours:
start: Sat Mar 27 19:21:59
stop: Sun Mar 28 08:25:07

What is the advantage of increasing the ml length or mi length with low coverage reads?...
Forum: 454 Pyrosequencing 03-26-2010, 06:23 PM
Replies: 3
Views: 2,943
Posted By Jordy224
Post 454assembly using Newbler: job time expectation?

Greetings

I would like to know how long should the following assembly to run using newbler?

The following are details:

gsAssebler
software version: 2.3
Data: 454 data ...
Forum: Bioinformatics 02-21-2009, 02:07 PM
Replies: 3
Views: 2,516
Posted By Jordy224
Yes, and the data was assembled into contigs. The...

Yes, and the data was assembled into contigs. The contigs have multiple gaps that I am attempting to resolve with 454 data.

For example I am using...

Mira with "ch_454_reads" to map against...
Forum: Bioinformatics 02-20-2009, 10:02 AM
Replies: 3
Views: 2,516
Posted By Jordy224
Solexa.abi and 454 seq data.

Greetings, I am new to assembly please bear with me .

Question: Is Mira or Velvet compatible with Solexa.abi.contigs and 454 reads?

Input:
ch_abi_contigs.fa
No of Sequences = 2527
Total...
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