1pm: Chief justice Arifin allows Shafee's request to submit tomorrow and for the defence to reply on Monday. Court adjourns for the day.
12.55pm: Court adjourns for lunch and the prosecution is to submit in the afternoon, but Shafee ( right ) asks his submission to be made tomorrow morning.
He says he intends to finish it tomorrow itself. The judges discuss the request.
12.40pm: Sangeet shows Anwar's cell was dirty before Anwar was placed there. She also pointed to the toilet in the cell and notes there was no sink inside.
The sink is outside the cell, she says in reply to questions from Justice Abdull Hamid on a police officer's conflicting testimony that he had heard Anwar brush his teeth, in contrast to the High Court judgment that states the police saw the opposition leader brushing his teeth.
"This shows that Anwar cannot have brushed his teeth outside, as the sink is outside the cell," she explains.
12.25pm: Ram says the sperm cells were not properly separated by the Chemistry Department.
He says the DNA evidence and scientific evidence is unreliable and hence there is no corroboration of Saiful's claim of being sodomised.
Ram points out that the hearing before the Federal Court is now in its third day, and he suggests the Court of Appeal in finding Anwar guilty and sentencing him within two days may have rushed the process.
He says as a result, the defence was not accorded a fair hearing in the Court of Appeal.
Ram finishes his submission and Sangeet continues with the defence.
Sangeet points to the lock-up diary to show the state of Anwar's cell during his detention.
12.10pm: Ram says there was no seminal stain on Saiful's trousers after the incident.
Justice Suriyadi asks if there is evidence that Saiful’s underwear was washed.
Ram says the underwear Saiful had used on the day of the alleged incident was washed but seminal stains were found on another underwear, which he did not use on that day.
"If seminal stain was found on that underwear, then there should also be similar stains on the trousers he used on the day of the incident," he adds.
Ram says the government chemist was biased in not wanting to answer questions from defence lawyers.
12.05pm : Outside the courtrrom, DAP's Ronnie Liu ( right in photo ) causes a commotion when he is blocked by court officers from entering the courtroom without a pass.
Liu claims he and others have been entering the courtroom without a pass for two days, and thus should not be stopped.
He has given his IC to the court officers and insists on waiting till he gets a pass to enter.
12.00pm: Hence, Ram says doubt should be given to the accused.
He says that the pro-forma report from the hospital states that Saiful resisted but there were no defensive wounds.
"Yet all four doctors, including three from HKL, state there are no signs of injury. Saiful says he was ravaged in a rough manner, resulting in excruciating pain, but there is no injury."
"The doctors said there ought to be injury if there was force and resistance as stated in the pro-forma.
"If K-Y jelly was used, they should accept the evidence of David Wells that there should be signs of injury due to the amount of force used," he adds.
11.50am: Ram says while Saiful claimed that the sodomy incident took place for five minutes when he testified in court, he, however, had told Supt Jude and the HKL doctor's that it went on for 30 minutes.
"If this is so (the longer duration), there will be signs of injury. This casts serious doubt on Saiful's testimony," he adds.
11.40am: Ram says the HKL doctor did not find any signs of tear or defensive wounds on Saiful.
"There is doubt to the factum of penetration on Saiful," he adds.
He points out that Dr Mohd Osman ( right ) also found the anus to be normal.
"How do you find semen in the rectum when there is no evidence of penetration," he says, adding that unless the items are different samples.
He argues that the trial judge and the Court of Appeal judges had erred in assuming that the right samples were found.
11.30am: DAP parliamentary leader Lim Kit Siang is in court with PKR's Sungai Petani MP Johari Abdul.
10.50am: Ram says there is clear misdirection, which has created a serious miscarriage of justice when the Court of Appeal did not take this into consideration.
He further submits that the evidence from Pusrawi doctor Dr Mohd Osman Abdul Hamid should be considered, and that if he was not telling the truth in the defence case, the prosecution can readily impeach him.
"However, Dr Osman's evidence was not rebutted, despite him stating that Saiful complained of pain in his anus for a week and that plastic was inserted in Saiful's anus."
10.45am: Anwar's supporters begin to swell, with some 100 now gathered outside the Palace of Justice.
Apart from supporters, there are also those selling pro-Anwar T-shirts, with the words "Rakyat Hakim Negara".
10.30am: Lembah Pantai MP Nurul Izzah Anwar enters the courtroom and takes a seat next to her younger sisters. Also in court is national laureate A Samad Said.
Ram Karpal continues with his submissions. He says this is a crucial issue of tampering.
According to defence expert witness Dr David Wells, he notes, the big plastic bag (P27) is not foolproof.
Ram adds investigation officer Supt Jude Pereira ( left ) also admitted the IGSO did not permit him to re-open exhibits that had already been sealed.
"The IGSO guidelines are designed to ensure the integrity of exhibits are not compromised by ensuring they are separately labelled and not mixed with other unrelated exhibits."
Justice Suriyadi Halim Omar, one of the five Federal Court judges, asks whether it is tampering the whole samples or just the cutting open of the big plastic bag, and Ram says it should be considered the whole samples as a result of the opening.
10.20am: Defence lawyer Ram Karpal says there is no reason for investigation officer Supt Jude Pereira to re-open the specimen when he went back to his office as it was already carefully sealed by the Hospital Kuala Lumpur doctors.
Pereira, he adds, cut open the P27 (the plastic bag containing the samples retrieved from Saiful).
"They (the samples) could have been compromised," he says.
"However, the appellate court defended this, saying Pereira was following the Inspector-General's Standing Orders (IGSO)."
Ram says Pereira was asked on the IGSO and the IO (investigation officer) agreed he did not follow the guidelines by the book.
"He says the items ought to be separated, when asked which paragraph in the IGSO says all items should be packed differently and not mixed with others.
"He had sealed all receptacles and placed them in separate plastic bags and sealed each plastic bag and placed it in the bigger plastic bag (P27), which was sealed again."
10.07am: Ram Karpal says the defence’s expert witness in the trial agreed that the 18 allele should have been reported.
"The 18 allele does not belong to ‘Male Y’. The presence of the DNA of a third party on those samples lends great weight to the defence contention that those samples must have been tampered with by third party. The IO (investigation officer Jude Periera) handled both samples.”
Ram also says there was a break in the chain of evidence.
Seah, he explains, received the samples (Saiful's) and also his trousers and underwear from Pereira on June 30 and July 1, 2008. She says she found traces of semen in B5, B7, B8 and B9.
9.51am: Defence lawyer Ram Karpal says the 18 allele is also found on the towel which was taken from the lock-up.
"The presence of the 18 allele cannot be from the doctors who examined it. The IO (investigation officer DSP Jude Blacious Pereira) may have contaminated it.
"This should be investigated further. Chemist Nor Aidora Saedon also did not investigate the presence of the 18 allele."
Apart from the towel, the 18 allele DNA profile was also found in Saiful's rectum.
"The fact that there was an 18 allele here (towel) and also in B9 (high rectum swab of Saiful) which was examined by Seah, belonged to the same person - possibly the IO - who must have tampered with both exhibits."
9.38am: Ram Karpal submits on the discovery of an 18 allele, which should have been reported. He says 'Male Y' is not the 18 allele.
"This ought to have been reported. This means it is contaminated and we do not know who it is. (Chemistry Department) Dr Seah Lay Hong ( left ) has failed to follow her guidelines (where she should report the matter)."
According to the Chemistry Department guidelines, the difference between one allele to another, for example between 18 and 19, if it exceeds by 15 to 25 percent, should be reported.
This 18 allele is reported to be 25 percent higher than the 19 allele.
9.36am: Court proceeding begins with Chief Justice Arifin presiding. Four other Federal Court judges take the bench.
Defence lawyer Ram Karpal Singh continues his submission from yesterday.
9.25am: Lead prosecutor Muhammad Shafee Abdullah walks into the courtroom.
The court is preparing to get ready while Anwar is seen discussing with Gopal Sri Ram and other lawyers.
The courtroom is already packed with people.
9.10am: Opposition Leader Anwar Ibrahim enters the courtroom. There is a slight commotion outside where loud shouting was heard.
Also in court is PKR president and wife Dr Wan Azizah Wan Ismail and her daughter and youngest son.
With Wan Azizah is her father, Wan Ismail Wan Mahmood.
8.55am: There are representatives from the various foreign embassies present, including United States, Australia, United Kingdom and the European Union.
Also Queens Counsel Mark Trowell is holding a watch for LawAsia and Law Council of Australia as well as the Inter-Parliamentary Union.
Among those in the public gallery is Wangsa Maju MP Tan Kee Kwong. Anwar Ibrahim's lead counsel Gopal Sri Ram arrives in court.
8.31am: People are trickling into the courtroom.
Among the opposition members already in court are Tumpat MP Kamarudin Jaafar, Batu Buruk assemblyperson Syed Azman Syed Mohamad and Kelana Jaya MP Wong Chen.
The international observers are seated on the extreme right of the court. The public gallery can fit 70 people but in the past two days, it is packed to the brim with 80 or more.
Deputy head of the prosecution division in the Attorney-General’s Chambers Mohd Hanafiah Zakaria is already in court.
For the defence, Sangeet Kaur Deo and Eric Paulsen are getting ready for the hearing.
8am: Only a small crowd of a dozen Anwar Ibrahim’s supporters is in the vicinity of the Palace of Justice in Putrajaya. Unlike yesterday, there are no protesters.
Those milling outside the court complex are mostly police personnel and journalists.
The court case is expected to resume at 9.30am.
7.35am: The prosecution team led by government-appointed lawyer, Muhammad Shafee Abdullah, is expected to seek a longer jail term for Opposition Leader Anwar Ibrahim in the Federal Court as the Sodomy II case enters its third day today.
Shafee is likely to submit either later this morning or in the afternoon on the issues raised by newly appointed Anwar's lead counsel, retired Federal Court judge Gopal Sri Ram.
The Umno-linked lawyer had told journalists outside court yesterday that "there was nothing new” that was raised by Anwar's defence team over the past two days.
Throughout the sodomy trial and the prosecution's appeal at the Court of Appeal last March, the case was handled by the late Karpal Singh who was tragically killed in a car crash early this year.
Initially, former Bar Council chairperson Sulaiman Abdullah, who led the defence when Anwar was charged in 2008, was slated to lead the PKR de facto leader's team.
However, he has not fully recovered following a surgery to his leg, and the defence team subsequently approached Gopal Sri Ram.
In the morning, defence lawyer and Karpal’s son, Ram Karpal Singh, is expected to continue his submission on the discrepancy in the DNA findings linking ‘Male Y’ to Anwar.
Yesterday, Ram had submitted on the possibility of the samples taken from alleged victim Mohd Saiful Bukhari Azlan's anus could be contaminated following the presence of an unidentified male DNA which was not reported by the Chemistry Department.
The unidentified DNA was found in the peri-anal and high rectum swab from Saiful.
He also said the samples were given to the department 96 hours after the alleged sodomy incident and yet it was found to be in "pristine" condition.
Ram ( right ) questioned how the samples from the low rectum and high rectum swabs could still be fresh when they were not kept in the freezer as recommended. Investigating officer DSP Jude Blacious Pereira had kept it in a steel cabinet at his office.
Sangeet Kaur Deo, another scion of the Karpal family and a member of Anwar’s huge defence team, also questioned the manner three items - a mineral water bottle, a toothbrush and a white towel - was retrieved from the opposition politician's cell when he was held overnight at the Kuala Lumpur police contingent headquarters.
She complained that there was deception and trickery adopted by the police in trying to get Anwar's DNA after the Permatang Pauh MP had refused to give his sample at the Hospital Kuala Lumpur.
Sangeet also argued that there was no evidence that Anwar had used those items.
Malaysiakini is covering the proceedings live.