User: eddie.im

gravatar for eddie.im
eddie.im130
Reputation:
130
Status:
Trusted
Location:
Brazil
Last seen:
6 years, 4 months ago
Joined:
6 years, 11 months ago
Email:
e**********@gmail.com

about me

Posts by eddie.im

<prev • 29 results • page 2 of 3 • next >
0
votes
1
answer
2.2k
views
1
answers
Answer: A: Nucleotide CDS from RefSeq?
... Get a list of protein acession number (in uniprot you can download then easily), then convert those to "EMBL CDS" through Uniprot "IDmaping" tab. Then use bpfetch (bioperl) with a loop. Thats how i did it.   while read accession_number ; do bp_fetch net::embl:${accession_number} ; done < acce ...
written 6.4 years ago by eddie.im130
0
votes
1
answer
1.3k
views
1
answers
Answer: A: further annotate gtf file from cufflinks?
... Take a look at this link: http://www.sequenceontology.org/gff3.shtml It provides an example of how to create a gff file with exon/intron and alternative splicing. Hope it helps. ...
written 6.4 years ago by eddie.im130
0
votes
1
answer
1.4k
views
1
answers
Comment: C: Tool to map sequences and get genomic coordenates
... I don't see how BLAT results would be different from BLAST, the same problem should arise from BLAT that is pieces of the sequences aligning everywhere. I will give it a shot however. Thanks. ...
written 6.5 years ago by eddie.im130
1
vote
1
answer
1.4k
views
1
answer
Tool to map sequences and get genomic coordenates
... Hello, Is there any software to map sequences against a genome and get genomic coordates/genomic ranges? I used several tools to get short sequences of ncRNA, but in the process i lost track of the genomic location of these, i have tried blast but it doens't perform very well, even when set to unga ...
R genomic ranges blast written 6.5 years ago by eddie.im130 • updated 6.5 years ago by Adrian690
0
votes
2
answers
6.4k
views
2
answers
Answer: A: Tools For Predicting Mirna Promoter Regions
... I dont't know about softwares to predict promoter regions of miRNA, as far as i know those are very specie specifc and usually won't perform very well. The most common aproach is to predict the miRNA sequences itself and then use a software like BPROM (http://linux1.softberry.com/berry.phtml?topic=b ...
written 6.5 years ago by eddie.im130
0
votes
1
answer
2.4k
views
1
answers
Comment: C: Genbank file format is wrong?
... Hi Zhaorong, thanks a lot! It helped me! ...
written 6.5 years ago by eddie.im130
2
votes
1
answer
2.4k
views
1
answer
Genbank file format is wrong?
... Hello, I'm having a hard time to understand the logic behind the Genkbank file format. In special about the "complement" feature, which doens't seems to make sense to me, can someone help me out? When i'm reading through a full genbank genome file, there is some annotations like: complement(1..200 ...
reverse genbank file written 6.5 years ago by eddie.im130 • updated 6.5 years ago by Biostar ♦♦ 20
0
votes
1
answer
1.5k
views
1
answers
Comment: C: Plant Microbe Interations
... I believe it's not possible. The interaction between plant-pathogen is very complex. The very best you can do is try to find a VERY close organism close to your fungi species and study expression levels on it, then you validate with RT-qPCR on your fungi. Yet it's very risky and the species must be ...
written 6.6 years ago by eddie.im130
1
vote
1
answer
1.5k
views
1
answers
Answer: A: Plant Microbe Interations
... As far as i know you can't. Each organism has his own level of expression which is regulated by many factors and differs from organism to organism even if the genes are orthologs. Fungi to Plant is a huge evolutionary leap, and even if they are in symbiosis their expression levels should probably be ...
written 6.6 years ago by eddie.im130
5
votes
2
answers
8.5k
views
2
answers
Answer: A: Could Any One Explain What Information Inside Sam File?
... Have you read [the documentation][1] about SAM files? There is a full description of what kind of information you will find inside a bam file. [1]: http://samtools.github.io/hts-specs/SAMv1.pdf ...
written 6.6 years ago by eddie.im130 • updated 13 months ago by _r_am31k

Latest awards to eddie.im

Commentator 6.4 years ago, created a comment with at least 3 up-votes. For C: DESeq differential expression
Appreciated 6.6 years ago, created a post with more than 5 votes. For A: Could Any One Explain What Information Inside Sam File?
Teacher 6.6 years ago, created an answer with at least 3 up-votes. For A: Could Any One Explain What Information Inside Sam File?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 974 users visited in the last hour