User: fusion.slope
fusion.slope • 240
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Posts by fusion.slope
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... Hello
I am trying to reconstruct the heavy chain and the light chain from two DNA sequences. I run for both purposes the command provided by IgBlastn:
database="my_path/to/db/"
optional_file="my_path/to/optional_file/"
igblastn -germline_db_V $database/human_igh_v -germ ...
written 4 months ago by
fusion.slope • 240
• updated
3 months ago by
Biostar ♦♦ 20
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... awesome! now null sequences model also for the mouse genome! ...
written 5 months ago by
fusion.slope • 240
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... Hello,
I am wondering if any of you here in the community knows the main differences between IgBlast and IMGT/V-QUEST.
From what I can see both of them can input a fasta sequence and return possile V genes J genes together with a potential D regions in the form of fasta sequence during B-cell re ...
written 5 months ago by
fusion.slope • 240
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... What i am doing i am lifting the coordinates of mouse to human as also the coordinates of human to mouse. Then on the lifted coordinates i calculate the conservation score using phasCons in UCSC table browser. I simulate also a set of sequences with similar GC content, size and nucleotide compositio ...
written 9 months ago by
fusion.slope • 240
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... do you think it is enough? ...
written 9 months ago by
fusion.slope • 240
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... Hello,
i have a list of DNA regions from mouse ESCs and I would like to know if these sequences are conserved also in Human. How can I do this? ...
written 9 months ago by
fusion.slope • 240
• updated
9 months ago by
JC ♦ 11k
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... Hello,
where can I find the annotation of the structure of each LINE1 element? I know that in repeatmasker is possible to find all the classes of transposons and retrotransposons and respective coordinates. But what about the annotation of their structure for each one?
Like for example:
for a put ...
written 9 months ago by
fusion.slope • 240
• updated
7 months ago by
Biostar ♦♦ 20
0
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... awesome Kevin, Just in time for my revision then :) Thanks a lot ...
written 11 months ago by
fusion.slope • 240
4
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290
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... Hello,
I am wondering if there is a database with annotated the structural variations as also the SNPs for cancer cell lines such as K562, HepG2 and MCF-7.
Any idea?
Thanks in advance ...
written 11 months ago by
fusion.slope • 240
• updated
11 months ago by
Kevin Blighe ♦ 66k
5
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... Hello,
does anybody of you has ever tried to generate null model of DNA sequences in mouse using the gkmSVM package? It works perfectly for human but for mouse it does not. I am wondering if any of you have ever used this package for mice and had the same problem.
The error problem when I use ...
written 23 months ago by
fusion.slope • 240
• updated
5 months ago by
sarahmcclymont • 20
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