User: Lyco

gravatar for Lyco
Lyco2.3k
Reputation:
2,260
Status:
Trusted
Location:
Germany
Last seen:
6 years, 10 months ago
Joined:
8 years, 3 months ago
Email:
l***********@indiatimes.com

Biochemist/Bioinformatician who knows a bit or two about protein sequence analysis, protein-protein interaction, and related topics.

Clearly a layman when it comes to python, ruby, xml, xml, xslt, and xwtf.

Currently working for a european biotech company, which means that I can't use half of the software/databases that people here call 'open' or 'free'.

Apparently the only person on BioStar who doesn't care about next-gen sequencing.

Posts by Lyco

<prev • 134 results • page 1 of 14 • next >
7
votes
1
answer
11k
views
5 follow
1
answer
Tool For Plotting Protein Architecture/Domains
... I am looking for a tool that can plot a protein domain graph (similar to how it is done in Pfam or Smart) from an input file containing domain coordinates and protein size. By searching the web, I found two tools that almost fit the bill: DOG (http://dog.biocuckoo.org) creates nice figures, but is ...
domain visualization protein protein-structure written 6.9 years ago by Lyco2.3k • updated 5.7 years ago by Michael Dondrup46k
0
votes
1
answer
3.3k
views
1
answers
Comment: C: Big Hierarchical Trees + Heatmap: Scripting Mev Or Suitable R Module
... Yes, we have tried heatmap.2 It is the best R solution we have seen so far, but not good enough. First, you can only add one colored indicator line, Second, there is a size limitation of about 3000 pixels (which might apply to everything R) . Given that you want the gene/experiment names to be reada ...
written 7.7 years ago by Lyco2.3k
2
votes
1
answer
3.3k
views
1
answer
Big Hierarchical Trees + Heatmap: Scripting Mev Or Suitable R Module
... We usually create heatmaps of hierachically clustered microarray data in MeV (multi-experiment viewer, part of the TM4 package). MeV might have its shortcomings, but it produces the nicest heatmap figures I have seen so far, allowing arbitrary sizes, different color schemes and additional class-indi ...
R bioconductor clustering heatmap written 7.7 years ago by Lyco2.3k • updated 7.7 years ago by Ly130
0
votes
3
answers
4.8k
views
3
answers
Answer: A: Residue Contact Map - Program And/Or Database
... A recent addition to the ranks of programs/servers for the task: COCOMAPS has been described in a recent article in Bioinformatics. The link to the online server ist https://www.molnac.unisa.it/BioTools/cocomaps/ ...
written 7.9 years ago by Lyco2.3k
0
votes
1
answer
3.2k
views
1
answers
Comment: C: How To Search Pdb For Sequence Regions That Are Resolved? (Edited)
... Dear Khader, great suggestions! Unfortunately, they don't solve my problem. pdbaa is what I am working with anyway. The SIFT is a nice resource that is news to me, but it doesn't help (see the example in the edited question). It is possible that atm2ali from the JOY package is the solution, but I am ...
written 7.9 years ago by Lyco2.3k
0
votes
2
answers
3.8k
views
2
answers
Comment: C: Analysis Of Low-Complexity Regions
... That is a good start. On the other hand, most protein regions are 'highly conserved in primates', just because there hasn't been enough time for accumulating mutations. In my opinion, a lineage-specific high conservation is meaningful only if e.g. the flanking regions have a lower conservation. ...
written 8.0 years ago by Lyco2.3k
2
votes
2
answers
3.8k
views
2
answers
Answer: A: Analysis Of Low-Complexity Regions
... I assume that you hope to attach some biological meaning to your variant, despite the fact that it is part of a compositionally biased region. As you certainly know (and Larry has mentioned), the majority of such protein regions are not particularly important. Antigenicity might be an issue, but pro ...
written 8.0 years ago by Lyco2.3k
0
votes
3
answers
2.9k
views
3
answers
Comment: C: Bioinformatics From Different Background With Different Education
... Could you briefly explain what 'community wiki' means, or where I can read anything about it? I checked the FAQ (in vain) and don't see any other help page or documentation linked on the Biostar pages ...
written 8.0 years ago by Lyco2.3k
4
votes
3
answers
4.8k
views
3
answers
Residue Contact Map - Program And/Or Database
... Can anybody recommend a good program/server for identifying contact residues from a given PDB-formatted file (protein-protein or protein-ligand contacts). No fancy graphics required, just a list of residues in molecule A that make a contact with residues of molecule B (assuming that a distance thres ...
pdb interaction protein written 8.0 years ago by Lyco2.3k
5
votes
12
answers
9.8k
views
12
answers
Comment: C: What Are The Obsolete Research Topics In Bioinformatics?
... I agree with the normalization problem being moot. I strongly disagree with "Microarrays are to a large extend being replaced by RNA-seq methods". This idea is perpetuated by software people, and hardcore technophiles. While microarray software development is clearly being replaced by RNA-seq develo ...
written 8.0 years ago by Lyco2.3k

Latest awards to Lyco

Guru 6.8 years ago, received more than 100 upvotes.
Supporter 6.8 years ago, voted at least 25 times.
Centurion 6.8 years ago, created 100 posts.
Autobiographer 6.8 years ago, has more than 80 characters in the information field of the user's profile.
Student 6.9 years ago, asked a question with at least 3 up-votes. For Tool For Plotting Protein Architecture/Domains
Popular Question 8.0 years ago, created a question with more than 1,000 views. For Residue Contact Map - Program And/Or Database
Commentator 8.0 years ago, created a comment with at least 3 up-votes. For C: What Are The Obsolete Research Topics In Bioinformatics?
Appreciated 8.0 years ago, created a post with more than 5 votes. For C: What Are The Obsolete Research Topics In Bioinformatics?
Appreciated 8.1 years ago, created a post with more than 5 votes. For Dna Multiple Alignment With Zero End-Gap Penalty
Student 8.1 years ago, asked a question with at least 3 up-votes. For Dna Multiple Alignment With Zero End-Gap Penalty
Teacher 8.1 years ago, created an answer with at least 3 up-votes. For A: Critical Issues In Pswms Usage
Popular Question 8.1 years ago, created a question with more than 1,000 views. For Phylogenetic Tree Of Sequenced Eukaryotes
Student 8.1 years ago, asked a question with at least 3 up-votes. For Phylogenetic Tree Of Sequenced Eukaryotes
Teacher 8.1 years ago, created an answer with at least 3 up-votes. For A: How Can I Profile A Multiple Alignment Result To Get A Logo Sequence To Represen
Teacher 8.1 years ago, created an answer with at least 3 up-votes. For A: Best Language For Introductory Programming Course From Within An Introduction Co
Good Answer 8.1 years ago, created an answer that was upvoted at least 5 times. For A: Best Language For Introductory Programming Course From Within An Introduction Co
Great Question 8.1 years ago, created a question with more than 5,000 views. For How Do People Go About Pubmed Text Mining
Student 8.1 years ago, asked a question with at least 3 up-votes. For How Do People Go About Pubmed Text Mining
Popular Question 8.1 years ago, created a question with more than 1,000 views. For How Do People Go About Pubmed Text Mining
Appreciated 8.1 years ago, created a post with more than 5 votes. For How Do People Go About Pubmed Text Mining
Good Question 8.1 years ago, asked a question that was upvoted at least 5 times. For How Do People Go About Pubmed Text Mining
Teacher 8.1 years ago, created an answer with at least 3 up-votes. For A: What Is The Status-Quo In Secondary Structure Prediction ?
Teacher 8.1 years ago, created an answer with at least 3 up-votes. For A: Should I Remove All Positions Containing A Gap In A Multiple Alignment Prior To
Appreciated 8.1 years ago, created a post with more than 5 votes. For A: Predicting Intrinsically Unstructured Areas In Protein Structures

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1079 users visited in the last hour