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Search: Posts Made By: sadiexiaoyu
Forum: Bioinformatics 04-03-2017, 02:46 AM
Replies: 0
Views: 747
Posted By sadiexiaoyu
questions about BINGO and CytoKEGG in cytoscape

Dear All,

I would like to use BINGO and CytoKEGG. However, it seems that I have to import GO file by myself, since my species is not in the cyptoscape BINGO. May I ask where can I download the GO...
Forum: Bioinformatics 02-07-2017, 02:25 AM
Replies: 0
Views: 817
Posted By sadiexiaoyu
asking about using bioperl to calculate ka ks

Dear All,

I would like to use bioperl script to calculate ka ks. I have already install bioperl at the root, since when I run perldoc Bio::SeqIO , it runs well. However, when I run perl...
Forum: Bioinformatics 01-25-2017, 05:05 PM
Replies: 5
Views: 1,523
Posted By sadiexiaoyu
hey, there

Hello,

thanks a lot for the reply!

I do it like this now, and it works!

from Bio import SeqIO
out = open('out.fa','w')
for seq_record in SeqIO.parse('original.fa','fasta'):
id =...
Forum: Bioinformatics 01-25-2017, 05:00 PM
Replies: 0
Views: 1,098
Posted By sadiexiaoyu
would like to convert aln to axt for Ka Ks calculator

Hello, everyone,

I would like to ask how to convert fasta file or .aln to .axt for ka ks calculation.

I have the .aln file now and have to convert it to .axt, and I have a huge amount of data...
Forum: Bioinformatics 01-24-2017, 10:05 PM
Replies: 5
Views: 1,523
Posted By sadiexiaoyu
help about the following python script

Hello, everybody,

I would like to run the following python script, but it gives me back error report.

from Bio import SeqIO
out=open("try_out.fasta","w")
for seq_record in SeqIO.parse...
Forum: Bioinformatics 01-20-2017, 05:15 PM
Replies: 1
Views: 1,361
Posted By sadiexiaoyu
Smile would like to extract cds region and concatenate fasta sequences

Hello, everyone,

Could you help me about the following issues?

I got hundreds of candidate genes which I am interested in and I have extracted the corresponding fasta sequences from...
Forum: Bioinformatics 11-13-2016, 10:54 PM
Replies: 2
Views: 1,297
Posted By sadiexiaoyu
inversion detection using raw reads

Hi, All,

I would like to use the raw genome pair-end data or the assembled scaffold and RAD sequencing data to detect inversion and the breaking point for special region in the genome and special...
Forum: Bioinformatics 09-29-2015, 11:28 AM
Replies: 0
Views: 735
Posted By sadiexiaoyu
novoalign parameters_alignment scoring options

Dear All,

I am confusing about the parameter in novoalign, the -t, -g, -x, I read the manual, and it seems that these three parameters can be used for setting mismatch when you map your reads to...
Forum: Bioinformatics 08-24-2015, 11:54 PM
Replies: 1
Views: 677
Posted By sadiexiaoyu
questions about KEGG manual

Dear All,

I would like to ask where can I find the manual for KEGG online version?


Thanks!

Cheers,

Sadiexiaoyu
Forum: Bioinformatics 07-07-2015, 01:17 AM
Replies: 1
Views: 733
Posted By sadiexiaoyu
Hi, angeloulivieri, I am also interested in...

Hi, angeloulivieri,

I am also interested in it!

May I ask have you already got the information?

Thanks!

Best,
Forum: Bioinformatics 07-07-2015, 01:11 AM
Replies: 0
Views: 681
Posted By sadiexiaoyu
questions about how to map pathway

Dear All,

I would like to do some investigations in pathway for some genes in different species. I have some candidate genes and also their corresponding gene sequences in different species, and I...
Forum: Bioinformatics 07-07-2015, 01:01 AM
Replies: 9
Views: 1,534
Posted By sadiexiaoyu
Dear All, The information here sounds...

Dear All,

The information here sounds interesting. I also would like to do some investigations in pathway in different species. I have some candidate genes and also their corresponding gene...
Forum: Bioinformatics 05-27-2015, 02:12 AM
Replies: 0
Views: 603
Posted By sadiexiaoyu
chromosome synteny

Dear All,

Anyone knows the software for detecting chromosome synteny between or among species? For example, I am interested in special chromosomes among different species, and would like to see...
Forum: Bioinformatics 05-26-2015, 09:58 PM
Replies: 8
Views: 1,090
Posted By sadiexiaoyu
Is there anybody know how to make syntenies for...

Is there anybody know how to make syntenies for chromosomes from different species?
Forum: Bioinformatics 05-26-2015, 12:39 PM
Replies: 8
Views: 1,090
Posted By sadiexiaoyu
Smile Thanks for these suggestions!

Thanks for these suggestions!
Forum: Bioinformatics 05-26-2015, 10:16 AM
Replies: 8
Views: 1,090
Posted By sadiexiaoyu
ahha, this is really helpful! But another...

ahha, this is really helpful!

But another question... is there any convenient way to view the alignment results? For example, which part of the chromosome of the species have common ancestor as...
Forum: Bioinformatics 05-26-2015, 09:15 AM
Replies: 8
Views: 1,090
Posted By sadiexiaoyu
Dear GenoMax, Thanks for your reply. ...

Dear GenoMax,

Thanks for your reply.

But I would like to not only compare chromosome between mouse and human, but also for other species which are not included in the list in the website... I...
Forum: Bioinformatics 05-26-2015, 07:39 AM
Replies: 8
Views: 1,090
Posted By sadiexiaoyu
chromosome comparison

Dear All,

I would like to ask is there any software can compare two chromosomes? For example, if I want to see how many genes are orthologues in one chromosome in Human and one chromosome in...
Forum: Bioinformatics 07-04-2014, 12:57 AM
Replies: 2
Views: 874
Posted By sadiexiaoyu
mapping contigs to reference genome

Dear All,

I got some contigs from de novo assemble. Now I would like to map these contigs to the reference genome. Is there any good software can do this?

Best,

Sadiexiaoyu
Forum: Bioinformatics 07-02-2014, 12:47 PM
Replies: 0
Views: 671
Posted By sadiexiaoyu
reference based de novo assemble

Dear All,

I get reads specifically for the target genes in different species. There is a genome which is close related to the species I am interested in will be used as a reference genome.

The...
Forum: Bioinformatics 06-30-2014, 12:13 PM
Replies: 0
Views: 832
Posted By sadiexiaoyu
parameter for fastq quality trimming by sliding window in Galaxy

Dear All,

I would like to use Fastq quality trimming by sliding window in Galaxy. However, I am confusing about the parameter setting. For example, Window size, step size, Maximum number of bases...
Forum: Bioinformatics 06-30-2014, 12:03 PM
Replies: 4
Views: 932
Posted By sadiexiaoyu
Yes, I agree with you. Thanks for the reply! :)

Yes, I agree with you. Thanks for the reply! :)
Forum: Bioinformatics 06-30-2014, 12:02 PM
Replies: 4
Views: 932
Posted By sadiexiaoyu
Ahha, yes, you are right!

Ahha, yes, you are right!
Forum: Bioinformatics 06-26-2014, 07:12 AM
Replies: 4
Views: 932
Posted By sadiexiaoyu
how to do target mapping efficiently

Dear All,

I would like to align the reads to some target genome region (for example, the gene I am interested in in the reference genome). Is there any efficient way to do this kind of target...
Forum: Bioinformatics 06-19-2013, 04:36 AM
Replies: 6
Views: 2,889
Posted By sadiexiaoyu
Hi, GenoMax, Yes, I tried. I build PATH...

Hi, GenoMax,

Yes, I tried. I build PATH first to go to samtools directory. And I also tried to build PATH to go to bcftools sub file. But neither worked out...
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