Anyone mine to share advance analysis of assembly ?

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Alternative software for gene and functional annotation and prediction

I'm looking for alternative software for gene and functional prediction, metabolic pathway construction and etc., is anyone willing to share their experience in yeast gene and functional prediction?

06 July 2012 8,721 2 View

Any nice gene and functional annotation software recommend by user experience?

There is too many sources of annotation software. Some can publish the complete genome even just using fully automatic annotation software. Yet, there is mis functional annotation. Different...

04 May 2012 8,642 0 View

What is the best idea to annotate a genome possess 70% gene slicing and 30% normal?

This is my first time handling such genome data.

04 May 2012 5,632 0 View

I face a technical problem on newbler GUI.

I cannot make newbler run GUI after installation and restart, can anyone can help me solve such an issue? I'm using CentOS 6.2 and Redhat 6. Both have the same problem >_

04 May 2012 3,747 0 View

Other than velvet, abyss, newbler, CABOG and amos - can anyone recommend a good open source software?

Looking for user experience feedback

04 May 2012 6,767 8 View

How solve such problem when convert newbler ace or std ace format file to amos bank format ?

During the conversion, the msg indicate the conversion fail, it's lock and lib not found. This situation also happend when I convert yeast velvet amos compatible to bank format.

04 May 2012 9,927 0 View

Any visualization software that shows pair end read information?

Do you know of any software that allows prediction and analyses of mis-assemble and QC of assembly result other than AMOS and CLC software?

04 May 2012 6,856 14 View

Is there any nice and recommended Gap Filling and gap extension software available?

I'm still newbie in NGS and my knowledge limited to few software. I'm trying to explorer to more software and method to gain my knowledge.

04 May 2012 8,323 0 View

Anyone know how to handle CABOG, assembler software. Can you explain how to run it ?

I failed to make it on either Illumina PE, Hiseq2000 (stuck at mery) and Roche 454 FLX (stuck to create overlap)

04 May 2012 443 7 View

Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence?

I am on the lookout for the Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence. Does anyone know where I can find it? Thank you in advance

03 March 2021 3,568 1 View

Is it possible for two human neuronal cell lines to have different gene sequence for the same protein?

I am looking at the ATP1A2 (Sodium/Potassium ATPase alpha subunit 2) in two human neuronal cell lines. Expression levels of this protein seems to be almost equal when detected by one antibody....

01 March 2021 3,607 3 View

Runs of nucleotides in Sanger sequencing?

I performed site directed mutagenesis, transformation, and then I sent out plasmids for Sanger sequencing and found out that there is extension of DNA just before the stop codon. I am not sure...

27 February 2021 547 3 View

Has anyone used the Illumina ITS1 primer sets?

Hi everyone, Illumina provides a list of primers to amplify with high taxonomic coverage the ITS1 region for further fungal sequencing, but I cannot find the exact amount necessary of each...

25 February 2021 6,969 3 View

How do you mesh a thin solid in Fluent?

Hello, I have used the shell function on SpaceClaim to create thin solids for the model I am studying. These are contained within an enclosure for my study. I chose this approach as it avoids the...

24 February 2021 8,856 3 View

Errors in DNA sequences?

I am trying to better understand the scope of DNA replication and sequencing errors, e.g. 1. I have seen similar error rates of 10e4 to 10e5 for cell & instrumental DNA replication,...

24 February 2021 4,397 3 View

Is it possible to define biogas as a fuel in the reformer process(scwg) in Homer software?

Hi every one Is it possible to define biogas as a fuel in the reformer process(scwg) in Homer software? Biogas fuel is not available in the options thanks

23 February 2021 6,518 3 View

I can detect my protein but the encoding DNA sequence has stop codons within. Should I ignore the stop codons?

I constructed a synthetic DNA library (scFv, VH-VL orientation) with a 3' reporter and 8x histag. I cloned and expressed this gene following which I performed an ELISA. The ELISA results suggested...

19 February 2021 7,006 5 View

What is the significance of (isolated) high titers of IgG anti GD1a antibodies in an older patient with polyneuropathy?

Remote history of Campylobacter infection with reactive arthritis, and Spitz nevus (UMP). Arthropod exposure in Zika/ChikV endemic area prior to emergence of length dependent, sensory PN with...

18 February 2021 8,719 1 View

Repository for capture-seq raw reads?

I am a research tech in a wildlife genetics group and my PI and I are trying to figure out how/where to put raw reads in a repository. We have capture-seq NGS from Rapid Genomics. The post-doc who...

17 February 2021 7,575 2 View

Vineet Jha

Annotation. That is some thing that is very trick and then their is no standard defination or answers to annotation.

K.s Sim

huh~ post at wrong one ?

However, i get what u meant...

My big problem keep arise on my head is the mis-annotation, mis-functional assign, and small gene.

better to set to 99bp