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Search: Posts Made By: Tsuyoshi
Forum: Bioinformatics 04-23-2013, 05:29 AM
Replies: 4
Views: 1,841
Posted By Tsuyoshi
Thank you mknut. I tried adding qcovs,...

Thank you mknut.

I tried adding qcovs, however, the output files did not contain the qcovs information. For example, if I input the command as outfmt "qacc sacc evalue bitscore qcovs", the output...
Forum: Bioinformatics 04-22-2013, 06:14 PM
Replies: 4
Views: 1,841
Posted By Tsuyoshi
Question Basic question about local BLASTP

Hello.

I am using local BLASTP program to blast my protein sequences (around 600 sequences) against other organism's whole proteome database. What I want to do is to filter the output by some...
Forum: Bioinformatics 04-11-2013, 07:47 PM
Replies: 15
Views: 6,637
Posted By Tsuyoshi
Thank you so much GenoMax, and yes I downloaded...

Thank you so much GenoMax, and yes I downloaded the protein dataset of Batrachochytrium dendrobatidis from JGI. The fasta file contains the sequences, however, the title of each sequence begins with...
Forum: Bioinformatics 04-11-2013, 07:29 PM
Replies: 15
Views: 6,637
Posted By Tsuyoshi
Thank you very much d1antho. I would like to try...

Thank you very much d1antho. I would like to try your method for retrieving other proteomes dataset.
Forum: Bioinformatics 04-11-2013, 05:46 AM
Replies: 15
Views: 6,637
Posted By Tsuyoshi
Yes, Thanks GenoMax, I neither got the full 8706...

Yes, Thanks GenoMax, I neither got the full 8706 sequences. I am going to try another methods. Thank you again.
Forum: Bioinformatics 04-11-2013, 04:58 AM
Replies: 15
Views: 6,637
Posted By Tsuyoshi
Thank you GenoMax! I did that but after...

Thank you GenoMax!
I did that but after clicking on "create file", an empty sequence.fasta file will be automatically downloaded. And there was an sentence said "Your session has expired. Please...
Forum: Bioinformatics 04-11-2013, 02:11 AM
Replies: 15
Views: 6,637
Posted By Tsuyoshi
Unhappy How to retrieve an organism's whole proteome from NCBI

HI.
I am suffering from a problem from retrieving the whole proteome dataset from NCBI for a while. Now I only have the taxonomic id of the organism (txid684364), and when I use the batch entrez of...
Forum: Bioinformatics 01-25-2013, 11:30 PM
Replies: 5
Views: 4,158
Posted By Tsuyoshi
Thank you Richard! I found another way to get...

Thank you Richard!
I found another way to get the sequences. Please find the descriptions here
http://edwards.sdsu.edu/labsite/index.php/robert/380-ncbi-sequence-or-fasta-batch-download-using-entrez
Forum: Bioinformatics 01-25-2013, 11:28 PM
Replies: 5
Views: 4,158
Posted By Tsuyoshi
Thank you maubp! I have tried to input the...

Thank you maubp!
I have tried to input the sequences from 10 to 100, and in different times, and the error occurred again and again. Therefore, I found an alternative way to get the famat sequences...
Forum: Bioinformatics 01-24-2013, 07:33 PM
Replies: 0
Views: 663
Posted By Tsuyoshi
Proteomics work problems

Hello!

Now I am working on a non-model organism and I would like to perform a subcellular organelle proteomics analysis. The only genome database I could use is another model organism that is...
Forum: Bioinformatics 01-24-2013, 07:18 PM
Replies: 5
Views: 4,158
Posted By Tsuyoshi
Problem with batch entrez

HI ALL!
Here is a very basic question, however, I have been frustrated by it.
I got a set of protein GI numbers, and I upload it to the Batch entrez tool in the website of NCBI...
Forum: Bioinformatics 09-10-2012, 04:22 AM
Replies: 11
Views: 3,674
Posted By Tsuyoshi
That's right. Anyway, I will try to extract the...

That's right.
Anyway, I will try to extract the accession numbers from NCBI.
Thank you very much Maubp !
Forum: Bioinformatics 09-10-2012, 04:12 AM
Replies: 11
Views: 3,674
Posted By Tsuyoshi
The sequences themselves are perfectly matched...

The sequences themselves are perfectly matched the submitted data of Chlamydomonas. I just have no idea what kind of IDs they are that the authors used.
Forum: Bioinformatics 09-10-2012, 04:02 AM
Replies: 11
Views: 3,674
Posted By Tsuyoshi
HI Maubp, But I still have a question about the...

HI Maubp,
But I still have a question about the protein ID, it seems like that there is no database name the proteins in that way, I mean, take several proteins as example, they are
...
Forum: Bioinformatics 09-10-2012, 03:45 AM
Replies: 11
Views: 3,674
Posted By Tsuyoshi
YEAP! I couldn't agree with you anymore....

YEAP!

I couldn't agree with you anymore. Many thanks!
Forum: Bioinformatics 09-10-2012, 03:38 AM
Replies: 11
Views: 3,674
Posted By Tsuyoshi
YES! What a stupid mistake I made. It succeeded...

YES!
What a stupid mistake I made. It succeeded now!

Thank you!
Forum: Bioinformatics 09-10-2012, 03:22 AM
Replies: 11
Views: 3,674
Posted By Tsuyoshi
Dear Maubp, Thanks for you reply. Yes I used...

Dear Maubp,
Thanks for you reply.
Yes I used -parse_seqids, and followed your suggestion, without the -parse_seqids, another error showed up,...
Forum: Bioinformatics 09-10-2012, 02:29 AM
Replies: 11
Views: 3,674
Posted By Tsuyoshi
Protein ID that blast could not identify

HI
I downloaded a proteome in fasta formater, which contains hundreds of proteins (http://labs.umassmed.edu/chlamyfp/index.php?content=help). And I want to blast against these proteins with my data...
Forum: Bioinformatics 09-09-2012, 05:09 AM
Replies: 11
Views: 37,360
Posted By Tsuyoshi
Dear NormSci, Thank you for your kind reply! ...

Dear NormSci,
Thank you for your kind reply!
I learned more useful commands in using blast+ from your reply, such as set the minimum identity percentage and especially the max_targe_seqs. It sounds...
Forum: Bioinformatics 09-09-2012, 04:55 AM
Replies: 11
Views: 37,360
Posted By Tsuyoshi
Dear Dario, Thank you very much for answering...

Dear Dario,
Thank you very much for answering this question, and you helped me a lot to resolve the problems of python several days ago.

In order to extract the best hit in results.txt, I have...
Forum: Bioinformatics 09-07-2012, 10:38 PM
Replies: 11
Views: 37,360
Posted By Tsuyoshi
Question how to output only one best-hit result using standalone blast

Hello
I am running standalone blast now to blastp a protein data set against a genome data.

Although I have set the best-hits filtering algorithm, namely, using -best_hit_overhang, and the value...
Forum: Bioinformatics 09-07-2012, 07:40 AM
Replies: 3
Views: 1,966
Posted By Tsuyoshi
Dear Dario, Thank you so much! It works!

Dear Dario,
Thank you so much!
It works!
Forum: Bioinformatics 09-07-2012, 07:38 AM
Replies: 3
Views: 1,966
Posted By Tsuyoshi
Dear Dario, Thank you for your kind answer! ...

Dear Dario,
Thank you for your kind answer!
Now it works well!
Thanks!
Forum: Bioinformatics 09-07-2012, 04:47 AM
Replies: 3
Views: 1,966
Posted By Tsuyoshi
Question Reciproca blast using Python

HI
I am running local Blast (version 2.2.6) on a mac machine, and I want to find the homologs between two protein database(named A and B) by reciprocal blast methods under python command lines.
I...
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