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anyone? please? sorry to pester, I assume its pretty basic stuff but I can't seem to find anything published on how to do it...

Thanks, This might be a silly question but do I measure all of the lines (horizontal and vertical) in the tree to get to the species I want? Or just the horizontal? So I measured everything for Alcedo azurea and come up with 0.1073 substitutions per site, is that the value for the branch length? I'm trying to put some branches of the tree into Newick format, so far i've worked out the code for the tree, now I just need to learn how to calculate the branch lengths to make it more accurate..

Hi, I'm trying to calculate the phylogenetic tree branch lengths for some kingfisher species, but I can't seem to find any information on how to do it. Here is the tree I am looking at KINGFISHERS so if i were to calculate the branch length for Alcedo azurea (the 6th from the top), what do I need to do? What would the branch length for this kingfisher be? Once I have one, I should be able to work out the rest. Thanks!

I'm working on a genetics assignment for uni and need some help to get me on the right track. It is about crossing Drosophila flys with veinless wings, forked bristles and a yellow body. The question is - Indicate whether the cross is (i) mutant females with wild type males, (ii)mutant males with wild type females or (iii) both(ie a recipricol cross), to produce an F1 generation that will enable you to determine if the traits are dominant or recessive and if they are sex linked. Draw mating diagrams and punnett squares to support your answer. As far as I can work out I think I need to be doing a recipricol cross? Can someone explain how this cross works to me I think i'm missing some important parts of it?! Should I cross the mutant female (XvwXvw, XfbXfb, XybXyb) with a wild male (X+Y, X+Y, X+Y) and then do the same but with a mutant male and wild female? Do I include the sex chromosomes XX and XYin the cross or just the traits? If these come out different this suggests that the trait is sex linked right? and then I should be able to work out recessive and dominant traits after that? I have scribbled down some working here hopefully you can read it. It takes me too long to type out these things! Does it look right? Sorry for all the questions, I think i'm confusing myself somewhere! Thanks

I've attched my sequence so far. It's in word so the colours come up. How does it look? I have the initiation and termination sites marked and the exons. Any suggestions of other important features that I should think about adding? I also had to choose and allelic variant and mark where it differs from the normal gene. Can you tell if i've done it correctly? This is the information I have on the variant from NCBI: .0001 LI-FRAUMENI SYNDROME 1 [TP53, ARG248TRP] Malkin et al. (1990) demonstrated that alterations of the TP53 gene occur not only as somatic mutations in human cancers, but also as germline mutations in some cancer-prone families. In 2 families with Li-Fraumeni syndrome-1 (151623), they identified a C-to-T mutation at the first nucleotide of codon 248, changing arginine to tryptophan (R248W). I found codon 248 in the amino acid seqence and highlighted that. Then I tried to find it in the nucleotide sequence by finding the amino acids surrounding it. eg, cgg®cgg®ccc(P). Some of them seem to fit and others dont. eg before the R there is supposed to be N, however the codon is cac which codes for H not N. Does that make sense? Am I doing something wrong? Thanks again! Sequence.doc

Thank you so much for showing me how to find initiation and termination points using the CDS information!! I had no idea what all of that part meant and was trying to do it by finding the points using the amino acid sequence, which was taking ages as I kept getting confused and had to start again. Your way is so much quicker! Another question, We are supposed to mark as many features as possible on the stand - so far I have the termination and initiation sites, what other kinds of features are there that can be marked? Just the different amino acids? Thanks again, i'm slowly getting through this!

Translation decodes the mRNA, so the sequence is a template DNA that needs to be converted to mRNA? Thats were the A is changed into U. So I should be finding complements for the sequence I have and then find the AUG initiation sites from that? How am I going? On the right track yet? haha Thankyou!

Hi, Ok, so i'm new to bioinformatics and don't really know what im doing! I am doing an assignment on tumor protein 53 and have been using the NCBI website and at the moment im stuck on a question. For the information below, I am supposed to find the nucleotide sequences of the gene (which is the sequences under the origin heading yes?) and the amino acid sequence data which I have been told is under the Features heading, though I have no idea how to read the information given! Any ideas? FEATURES Location/Qualifiers source 1..2331 /organism="Homo sapiens" /mol_type="mRNA" /db_xref="taxon:9606" /chromosome="17" /map="17p13.1" gene 1..2331 /gene="TP53" /gene_synonym="FLJ92943; LFS1; p53; TRP53" /note="tumor protein p53" /db_xref="GeneID:7157" /db_xref="HGNC:11998" /db_xref="MIM:191170" exon 1..441 /gene="TP53" /gene_synonym="FLJ92943; LFS1; p53; TRP53" /inference="alignment:Splign" /number=5a STS 243..558 /gene="TP53" /gene_synonym="FLJ92943; LFS1; p53; TRP53" /standard_name="GDB:178567" /db_xref="UniSTS:155019" STS 243..486 /gene="TP53" /gene_synonym="FLJ92943; LFS1; p53; TRP53" /standard_name="GDB:363689" /db_xref="UniSTS:156784" STS 243..353 /gene="TP53" /gene_synonym="FLJ92943; LFS1; p53; TRP53" /standard_name="GDB:177724" /db_xref="UniSTS:154952" CDS 279..923 /gene="TP53" /gene_synonym="FLJ92943; LFS1; p53; TRP53" /note="isoform f is encoded by transcript variant 7; p53 tumor suppressor; phosphoprotein p53; p53 antigen; p53 transformation suppressor; transformation-related protein 53" /codon_start=1 /product="tumor protein p53 isoform f" /protein_id="NP_001119589.1" /db_xref="GI:187830909" /db_xref="GeneID:7157" /db_xref="HGNC:11998" /db_xref="MIM:191170" /translation="MFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRC PHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHY NYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKK GEPHHELPPGSTKRALPNNTSSSPQPKKKPLDGEYFTLQMLLDLRWCYFLINSS" STS 360..434 /gene="TP53" /gene_synonym="FLJ92943; LFS1; p53; TRP53" /standard_name="PMC340938P3" /db_xref="UniSTS:273171" exon 442..554 /gene="TP53" /gene_synonym="FLJ92943; LFS1; p53; TRP53" /inference="alignment:Splign" /number=6 exon 555..664 /gene="TP53" /gene_synonym="FLJ92943; LFS1; p53; TRP53" /inference="alignment:Splign" /number=7 STS 635..833 /gene="TP53" /gene_synonym="FLJ92943; LFS1; p53; TRP53" /standard_name="PMC310707P2" /db_xref="UniSTS:272633" STS 639..713 /gene="TP53" /gene_synonym="FLJ92943; LFS1; p53; TRP53" /standard_name="GDB:190076" /db_xref="UniSTS:155620" exon 665..801 /gene="TP53" /gene_synonym="FLJ92943; LFS1; p53; TRP53" /inference="alignment:Splign" /number=8 exon 802..875 /gene="TP53" /gene_synonym="FLJ92943; LFS1; p53; TRP53" /inference="alignment:Splign" /number=9 exon 876..935 /gene="TP53" /gene_synonym="FLJ92943; LFS1; p53; TRP53" /inference="alignment:Splign" /number=10b exon 936..1042 /gene="TP53" /gene_synonym="FLJ92943; LFS1; p53; TRP53" /inference="alignment:Splign" /number=11 exon 1043..2331 /gene="TP53" /gene_synonym="FLJ92943; LFS1; p53; TRP53" /inference="alignment:Splign" /number=12 STS 1194..1310 /gene="TP53" /gene_synonym="FLJ92943; LFS1; p53; TRP53" /standard_name="D17S1678" /db_xref="UniSTS:82485" STS 1651..1797 /gene="TP53" /gene_synonym="FLJ92943; LFS1; p53; TRP53" /standard_name="D17S1506E" /db_xref="UniSTS:151711" STS 2186..2262 /gene="TP53" /gene_synonym="FLJ92943; LFS1; p53; TRP53" /standard_name="WI-20715" /db_xref="UniSTS:59997" polyA_signal 2295..2300 /gene="TP53" /gene_synonym="FLJ92943; LFS1; p53; TRP53" polyA_site 2312 /gene="TP53" /gene_synonym="FLJ92943; LFS1; p53; TRP53" ORIGIN 1 tgaggccagg agatggaggc tgcagtgagc tgtgatcaca ccactgtgct ccagcctgag 61 tgacagagca agaccctatc tcaaaaaaaa aaaaaaaaaa gaaaagctcc tgaggtgtag 121 acgccaactc tctctagctc gctagtgggt tgcaggaggt gcttacgcat gtttgtttct 181 ttgctgccgt cttccagttg ctttatctgt tcacttgtgc cctgactttc aactctgtct 241 ccttcctctt cctacagtac tcccctgccc tcaacaagat gttttgccaa ctggccaaga 301 cctgccctgt gcagctgtgg gttgattcca cacccccgcc cggcacccgc gtccgcgcca 361 tggccatcta caagcagtca cagcacatga cggaggttgt gaggcgctgc ccccaccatg 421 agcgctgctc agatagcgat ggtctggccc ctcctcagca tcttatccga gtggaaggaa 481 atttgcgtgt ggagtatttg gatgacagaa acacttttcg acatagtgtg gtggtgccct 541 atgagccgcc tgaggttggc tctgactgta ccaccatcca ctacaactac atgtgtaaca 601 gttcctgcat gggcggcatg aaccggaggc ccatcctcac catcatcaca ctggaagact 661 ccagtggtaa tctactggga cggaacagct ttgaggtgcg tgtttgtgcc tgtcctggga 721 gagaccggcg cacagaggaa gagaatctcc gcaagaaagg ggagcctcac cacgagctgc 781 ccccagggag cactaagcga gcactgccca acaacaccag ctcctctccc cagccaaaga 841 agaaaccact ggatggagaa tatttcaccc ttcagatgct acttgactta cgatggtgtt 901 acttcctgat aaactcgtcg taagttgaaa atattatccg tgggcgtgag cgcttcgaga 961 tgttccgaga gctgaatgag gccttggaac tcaaggatgc ccaggctggg aaggagccag 1021 gggggagcag ggctcactcc agccacctga agtccaaaaa gggtcagtct acctcccgcc 1081 ataaaaaact catgttcaag acagaagggc ctgactcaga ctgacattct ccacttcttg 1141 ttccccactg acagcctccc acccccatct ctccctcccc tgccattttg ggttttgggt 1201 ctttgaaccc ttgcttgcaa taggtgtgcg tcagaagcac ccaggacttc catttgcttt 1261 gtcccggggc tccactgaac aagttggcct gcactggtgt tttgttgtgg ggaggaggat 1321 ggggagtagg acataccagc ttagatttta aggtttttac tgtgagggat gtttgggaga 1381 tgtaagaaat gttcttgcag ttaagggtta gtttacaatc agccacattc taggtagggg 1441 cccacttcac cgtactaacc agggaagctg tccctcactg ttgaattttc tctaacttca 1501 aggcccatat ctgtgaaatg ctggcatttg cacctacctc acagagtgca ttgtgagggt 1561 taatgaaata atgtacatct ggccttgaaa ccacctttta ttacatgggg tctagaactt 1621 gacccccttg agggtgcttg ttccctctcc ctgttggtcg gtgggttggt agtttctaca 1681 gttgggcagc tggttaggta gagggagttg tcaagtctct gctggcccag ccaaaccctg 1741 tctgacaacc tcttggtgaa ccttagtacc taaaaggaaa tctcacccca tcccacaccc 1801 tggaggattt catctcttgt atatgatgat ctggatccac caagacttgt tttatgctca 1861 gggtcaattt cttttttctt tttttttttt ttttttcttt ttctttgaga ctgggtctcg 1921 ctttgttgcc caggctggag tggagtggcg tgatcttggc ttactgcagc ctttgcctcc 1981 ccggctcgag cagtcctgcc tcagcctccg gagtagctgg gaccacaggt tcatgccacc 2041 atggccagcc aacttttgca tgttttgtag agatggggtc tcacagtgtt gcccaggctg 2101 gtctcaaact cctgggctca ggcgatccac ctgtctcagc ctcccagagt gctgggatta 2161 caattgtgag ccaccacgtc cagctggaag ggtcaacatc ttttacattc tgcaagcaca 2221 tctgcatttt caccccaccc ttcccctcct tctccctttt tatatcccat ttttatatcg 2281 atctcttatt ttacaataaa actttgctgc cacctgtgtg tctgaggggt g Then i'm supposed to mark sites of initiation and termination on the nucleotide sequence. I know the initiation codon is atg, so does that mean whenever I find atg in the sequence it is an initiation site? For example in this line, is the place ive put the (()) around an initiation site? 1 tgaggccagg ag((atg))gaggc tgcagtgagc tgtgatcaca ccactgtgct ccagcctgag How many initiation and termination sites should there be? I'm so confused! Hopefully someone can set me straight, I tried talking to my lecturer but he isnt very good with english and has a hard time explaining. I've been trying to learn this course from a text book and can only get so far. Thanks!