SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 29
Search took 0.00 seconds.
Search: Posts Made By: rdu
Forum: Bioinformatics 12-26-2011, 07:02 PM
Replies: 7
Views: 2,941
Posted By rdu
Sorry, I didnt get a chance to back here. ...

Sorry, I didnt get a chance to back here.

Actually, I'm doing this. I downloaded 20 different bacteria genomes from NCBI website. These genome gene annotation files are ready there. Then I cut...
Forum: Bioinformatics 12-18-2011, 03:40 PM
Replies: 7
Views: 2,941
Posted By rdu
blastx parameters for CDS finding

I'm thinking to use BLASTX to find CDS (protein coding sequence) regions on genomes. How can I set the parameters to let BLASTX put big penalty on a stop codon found? Any experience or any useful...
Forum: Bioinformatics 11-03-2011, 07:31 PM
Replies: 0
Views: 1,359
Posted By rdu
Align genomic DNA sequence to protein database?

Hi,

I'm interested in doing metagenome functional annotation. I found in some papers, researchers directly align genomic DNA sequence to a protein database, such as COG. I'm thinking, since there...
Forum: Bioinformatics 04-28-2011, 10:22 AM
Replies: 0
Views: 1,449
Posted By rdu
BLAST result

Hi,

Greetings!

Anyone happened to know the tricks by using 'Effective Search Space' (ESS) in the BLAST result to get the E-value.

I just simply tried the Karlin-Altschul Statistics:...
Forum: Bioinformatics 04-13-2011, 08:54 AM
Replies: 0
Views: 1,542
Posted By rdu
BLAST xdrop set

Anyone happened to know the default values for xdrop_gap, xdrop_gap_final, xdrop_ungap when you take BLAST running? Thanks
Forum: Bioinformatics 03-16-2011, 01:22 PM
Replies: 0
Views: 996
Posted By rdu
Seqmap34 output

Hi Guys,

I downloaded a RNAseq data from http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM543645.

You can see after sequencing it being mapped to a genome by using
Seqmap34. I have no...
Forum: Bioinformatics 02-16-2011, 12:46 PM
Replies: 6
Views: 2,756
Posted By rdu
My output is generated by AB WT Pipeline with...

My output is generated by AB WT Pipeline with .max format.

I tried by 1:22 - 1:22, 23 - X, 24 - Y, 25 - MT and got 755 reads annotated by gene ids from "X", 57 from "Y", and 27 from "MT". Is it...
Forum: Bioinformatics 02-15-2011, 06:10 PM
Replies: 6
Views: 2,756
Posted By rdu
Thanks again. It's really helpful.

Thanks again. It's really helpful.
Forum: Bioinformatics 02-15-2011, 01:38 PM
Replies: 6
Views: 2,756
Posted By rdu
Thank you very much! 1:22 - 1:22 23 - X ...

Thank you very much!

1:22 - 1:22
23 - X
24 - Y
25 - MT

Is it correct by what you meant?
Forum: Bioinformatics 02-15-2011, 12:26 PM
Replies: 6
Views: 2,756
Posted By rdu
human chromosome index

Hi,

I got an alignment output, for each read which has a human chromosome index and its location. I'm trying to convert these records to corresponding gene ids.

Now, the question is in the...
Forum: Bioinformatics 02-15-2011, 12:14 PM
Replies: 9
Views: 40,975
Posted By rdu
Bioconductor package "biomaRt" also could do...

Bioconductor package "biomaRt" also could do it.
Forum: Bioinformatics 02-10-2011, 03:48 PM
Replies: 0
Views: 2,394
Posted By rdu
assign chromosome location to gene id

Hi,

I used 'getBM' function in Bioconductor package 'biomaRt' to retrieve gene ids based on known chromosome locations.

The question is getBM just only return one gene even the query is...
Forum: Bioinformatics 02-08-2011, 01:30 PM
Replies: 0
Views: 1,055
Posted By rdu
alignment output refid recognition

I have a .MAX alignment output file, which was generated by AB WT Pipeline. The reads were aligned to the human hg18 (NCBI Build 36) genome.

One alignment of the .MAX is like:
...
Forum: Bioinformatics 01-27-2011, 10:59 AM
Replies: 3
Views: 12,818
Posted By rdu
Hi apratap, Thank you. Your anwser sounds...

Hi apratap,

Thank you. Your anwser sounds reasonable. If I know some related futher, will also share with you. Have a nice day.
Forum: Bioinformatics 01-26-2011, 09:06 AM
Replies: 3
Views: 12,818
Posted By rdu
"N"s in DNA sequence data

I found there're many "N"s in a initial DNA genome sequence data, like:

CTGAAATCACTACTTTCCTTGTTAGGCTCGGCGCATGTGTTAAGTAGNNN
NTTATANNCNGNNNAGNATTTATNNNNNNNNCTTNNNNNNCGGTTATATG

What's the...
Forum: Bioinformatics 01-25-2011, 06:25 AM
Replies: 3
Views: 5,271
Posted By rdu
Got it, thank you!

Got it, thank you!
Forum: Bioinformatics 01-24-2011, 11:46 AM
Replies: 3
Views: 5,271
Posted By rdu
BLAST output parsing in R?

Is there a package, or some special way to parse BLAST output by programming in R? Thanks.
Forum: General 01-14-2011, 11:32 AM
Replies: 2
Views: 2,014
Posted By rdu
I dont have an answer. Instead, I suggest you to...

I dont have an answer. Instead, I suggest you to switch your question to "Bioinformatics" section, because I can get replies soon after my questions being posted there. Good luck!
Forum: Bioinformatics 01-14-2011, 11:13 AM
Replies: 4
Views: 7,220
Posted By rdu
Thanks. Let me take a try. Have a good day to...

Thanks. Let me take a try.
Have a good day to everyone!
Forum: Bioinformatics 01-14-2011, 09:45 AM
Replies: 4
Views: 7,220
Posted By rdu
Thanks. Yes, I understand the input should...

Thanks.

Yes, I understand the input should be a standard DNA sequence. The thing confusing me is this DNA sequence should only compose of protein coding parts, or it just a common DNA sequence....
Forum: Bioinformatics 01-13-2011, 05:56 PM
Replies: 4
Views: 7,220
Posted By rdu
query required by BLASTX

From the website, "BLASTX search protein databases using a translated nucleotide query." What does "a translated nucleotide query" really mean here? Shouldn't be a initial genomic DNA sequence,...
Forum: Bioinformatics 01-12-2011, 11:39 AM
Replies: 4
Views: 3,835
Posted By rdu
Appreciate, dschika and anna. The mistake I...

Appreciate, dschika and anna.

The mistake I made is I wasn't at the correct directory. After I switched there "makeblastdb" did take actions. But just like what you both pointed out, the...
Forum: Bioinformatics 01-10-2011, 08:01 PM
Replies: 4
Views: 3,835
Posted By rdu
question on making BLAST db

Hi,

I'm trying to make a BLAST database. The fasta file was downloaded from ftp://ftp.theseed.org/genomes/SEED/SEED.fasta.gz. Then I used commond line: makeblastdb -in seed.fasta -out seeddb...
Forum: Bioinformatics 01-06-2011, 11:20 AM
Replies: 2
Views: 1,340
Posted By rdu
Very helpful! Thanks a lot!

Very helpful! Thanks a lot!
Forum: Bioinformatics 01-06-2011, 09:20 AM
Replies: 2
Views: 1,340
Posted By rdu
simple questions

Hi guys,

I started and got two simple questions:

1. I got a example of initial DNA sequence like
234301 gattggccag cgggaagggc atctcgatgc ccaggacctt gccgtggacg actgtcttca
My question is...
Showing results 1 to 25 of 29

 


All times are GMT -8. The time now is 06:01 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO