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Search: Posts Made By: Lyn Hsiong
Forum: Bioinformatics 11-14-2013, 03:50 AM
Replies: 1
Views: 1,156
Posted By Lyn Hsiong
How to use codeml to calculate ω ratios of internal branches "iteratively"

Hi, my dear guys, I have a question about ω ratio calculation by codeml for my specific purpose.

I have constructed a ML tree (for a gene family), and I only focus on the substitutions along the...
Forum: Bioinformatics 06-06-2013, 06:24 PM
Replies: 2
Views: 5,867
Posted By Lyn Hsiong
Thank you for your reply! Do you mean the...

Thank you for your reply!
Do you mean the function Bio::Search::SearchUtils::tile_hsps($hit)?
I have checked the usage, but I am afraid that I still need a simple practical example, even if only...
Forum: Bioinformatics 06-06-2013, 05:45 PM
Replies: 2
Views: 1,827
Posted By Lyn Hsiong
Thanks for your reply! I tried the...

Thanks for your reply!
I tried the $hit->next_hsp before, but running the script still informed me the same error. However, today I have just reruned the script, both $hit->next_hsp and $hit->hsp...
Forum: Bioinformatics 06-05-2013, 09:26 PM
Replies: 2
Views: 1,827
Posted By Lyn Hsiong
Errors in my bioperl script. Thanks in advance!

Dear friends:

I have a blast report, and want to extract following information for each result(query): the Query_name, hit_number, name and description of the hit(HSP) with the highest identity.
...
Forum: Bioinformatics 05-24-2013, 07:17 AM
Replies: 2
Views: 5,867
Posted By Lyn Hsiong
how to merge contiguous blast hsps! (-m 8 tab)

Hi, guys!

I performed blastx (-m 8) using a query file of many sequences, and for each target sequence, the output contains many fragmental hsps of significance, and these hsps have overlap...
Forum: Bioinformatics 04-18-2013, 05:53 PM
Replies: 2
Views: 1,962
Posted By Lyn Hsiong
thank you for your reply! actually, what you...

thank you for your reply!
actually, what you mentioned may typify one of the cases. then here i performed a tblastx using two genome sequences and found some of the hits per query had close...
Forum: Bioinformatics 04-18-2013, 09:24 AM
Replies: 2
Views: 1,962
Posted By Lyn Hsiong
how to concatenate blast results (m8) via setting threshold of distance between hits

hi, dear guys

I performance blastn (-m 8) using a query file of many sequences, and for each query sequence, the output contains many fragmental hits of significance.

however, these hits have...
Forum: Bioinformatics 12-27-2012, 04:53 AM
Replies: 4
Views: 2,525
Posted By Lyn Hsiong
I have sent several emails to the developers, but...

I have sent several emails to the developers, but it informed me [Your message to cedric@uta.edu was rejected by the recipient domain. The error that the other server returned was: " SMTP error, RCPT...
Forum: Bioinformatics 12-22-2012, 07:19 PM
Replies: 4
Views: 2,525
Posted By Lyn Hsiong
where to download RepClass! the tool on sourceforge is unavailable now!

the software on http://sourceforge.net/projects/repclass/files/ is unavailable now:confused:, cause the tar.gz file downloaded is totally empty!

I don't know where to get the tool, hope someone...
Forum: Bioinformatics 12-11-2012, 01:38 AM
Replies: 40
Views: 21,282
Posted By Lyn Hsiong
thank you very much! but i don't know how to deal...

thank you very much! but i don't know how to deal with the .pm file (i suppose you meant the file "RepModelConfig.pm"). the file only contains Pre-installed programs' paths (perl, recon, repeatmasker...
Forum: Bioinformatics 11-27-2012, 10:13 PM
Replies: 0
Views: 1,007
Posted By Lyn Hsiong
Hi, Anybody used P-Clouds? thanks

I have studied P-Clouds——a tool to annotate repeat sequences in genomes ——for several days, but many problems troubled me!

when I changed the parameters in the control file, it always reported...
Forum: Bioinformatics 11-27-2012, 08:57 PM
Replies: 15
Views: 7,995
Posted By Lyn Hsiong
Hi, I think you could try to change the engine by...

Hi, I think you could try to change the engine by "-engine abblast". I don't know why, but it works for me when I have a similar problem.
lyn
Forum: Bioinformatics 11-27-2012, 08:32 PM
Replies: 40
Views: 21,282
Posted By Lyn Hsiong
Hi, my repeatmoderler run very slowly too, and...

Hi, my repeatmoderler run very slowly too, and the input genome is 300M. Maybe the abblast, by default, also used only 1 cpu, so I assigned 10 by "-num_threads 10" like you, however, the...
Forum: Introductions 09-26-2011, 01:42 AM
Replies: 2
Views: 2,207
Posted By Lyn Hsiong
Smile hello, i am a novice but interested in NGS!

how many kinds of NGS are there nowadays? and whether the sequencing efficiency and ability of each of these approaches exist corresponding sample bias, that is to say, maybe some approches are more...
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